Tehran's streets at the height of the morning rush hour resemble a vast, sprawling car park. Bumper-to-bumper traffic, much of it stationary, the acrid steam of a thousand exhausts hanging in the cold winter air. If you wanted to kill someone, this would be the moment to do it: when they are stuck in their cars – sitting targets.

At 7.40am last Monday, in north Tehran's Aghdasieh district, a motorcycle threaded its way through the long lines of cars on Artesh Boulevard. It edged up to a silver Peugeot 405, hesitating alongside for moment, before moving off into the maze of vehicles. A few seconds later there was a bang from the side of the Peugeot, as a small bomb stuck on to the window detonated, killing one of the men inside. The driver and a woman passenger were wounded.

At the same time, a few kilometres to the west, an identical attack was under way. A motorcycle came up beside another Peugeot and then moved on, but this time a man immediately jumped out of the car, ran around to let a woman out on the other side, and both of them managed to scramble a couple of metres from the car before the bomb went off. They were bloodied, but survived.

The dead man was Majid Shahriari, a senior Iranian nuclear scientist. The head of Iran's nuclear programme, Ali Akbar Salehi, who attended his funeral, said Shahriari had been "in charge of one of the great projects" at Iran's atomic energy agency – a project he did not describe any further.

The wounded man, Fereydoun Abbasi, was a 52-year-old nuclear scientist working for Iran's defence ministry, one of "Iran's few experts on fissile isotopes and the ministry's laser expert". He is also named in a UN security council sanctions resolution as working on "banned nuclear activities" with Mohsen Fakhrizadeh, the scientist suspected by inspectors at the International Atomic Energy Agency of running Iran's secret nuclear weapons programme. The wives of both scientists were wounded in the attacks.

The attacks had clear echoes of the unsolved assassination in January this year of one of their colleagues, particle physicist Masoud Alimohammadi. He was killed in north Tehran on his way to work, at about the same time of the morning, by a bomb strapped to a motorcycle. After his death, to the surprise of many of his students, it was reported that he also had links with Iran's nuclear programme.

If there were any doubts after Alimohammadi's killing back in January, there could be none after last week's double attack. Someone is trying to kill nuclear scientists linked to Iran's defence establishment – the people most likely to be involved in the covert side of Iran's nuclear programme, the making of nuclear weapons.

In the febrile atmosphere of Iranian underground politics, speculation quickly spread that the dark forces of the state were at work against would-be dissidents, leakers or defectors, but those rumours quickly evaporated. The Islamic Republic has many other ways of taking people it suspects out of circulation. It has little to gain by sacrificing the nation's must strategic asset – its nuclear know-how, the teachers of a new generation of atomic scientists. After last week, that new generation must be wondering whether to change career.

The Tehran regime itself had little doubt over who was to blame. President Mahmoud Ahmadinejad quickly pointed the finger at "western governments and the Zionist regime".

Ahmadinejad blames almost every national setback on the same culprits, but in this case there were no snorts of derision from the security analysts and intelligence experts in the west, but rather murmurs of assent.

There is general agreement that the nature of the simultaneous attacks was too sophisticated to be entirely home-grown – the work of the handful of groups who harry the Islamic Republic around its ethnic edges, like the Sunni Jundullah group, the Kurdish rebels in the north-east, or the People's Mujahedin (which has vowed to give up violence to win removal from the US state department's list of terrorist organisations).

The assassination had the hallmark of well-practised professionals. The explosives were shaped to focus the blast and fire a hail of projectiles into the car at an individual target, with minimal "collateral damage". The targets were obviously carefully chosen and the attack would have required weeks of surveillance. So even if local assassins were involved, the questions of who trained and funded them and assigned the targets would remain.

Time magazine last week claimed to have been given details of the attack from "a western intelligence expert with knowledge of the operation" and asserted that it "carried the signature of Israel's Mossad".

It is certainly true that, while the discovery of any involvement in the killings of civilian scientists would be career-endingly embarrassing for the CIA or MI6, the Mossad is known for such exploits. It is widely believed to have killed scientists working on Iraq's nuclear programme in the 1980s.

The outgoing Mossad director, Meir Dagan, has stepped up the use of assassinations against Israel's enemies, and has won plaudits for doing so. The Israel Hayom news website remarked on the occasion of Dagan's retirement: "[He] will be leaving an organisation that is far sharper and more operational than the organisation he received, and all of the accusations from Tehran yesterday are a good indication of that. Iran will be the focal point for the next Mossad director, too."

If it does indeed turn out that the Mossad was involved, the bloodshed in the middle of Tehran represents a bloody episode in a secret war over Iran's nuclear programme that has been under way for years.

It has come at a time when diplomacy is at a standstill. Officials from six major powers – the US, Britain, France, Russia, China and Germany – are due to meet Iranian chief negotiator Saeed Jalili in Geneva tomorrow for the first time in more than a year. But expectations are low. Iran has shown no interest in complying with UN demands to cease the enrichment of uranium, despite four sets of sanctions. Tehran has also turned down a deal to swap some of its stock of low-enriched uranium for ready-made fuel rods it urgently needs for a medical research reactor.

Military action has been contemplated for years, in Washington and Tel Aviv, but both have concluded that air strikes on nuclear sites would have an uncertain and far from fatal impact on Iran's programme, would unleash years of unpredictable, painful reprisals, and would probably spur Tehran on in the quest to develop nuclear weapons.

The Pentagon has contingency plans, but there is no real likelihood of the US starting a third war in the region any time soon. Israel is another matter. Israeli officials say they are well aware of the downsides of military action, but they insist that none compares with the "existential threat" posed to their country by a nuclear-armed Iran.

Without giving a green light, the US has supplied the tools Israel would need to do the job. One of the US cables made public by WikiLeaks describes a meeting of a US-Israeli joint political military group in November last year. It said: "The GOI [Government of Israel] described 2010 as a critical year – if the Iranians continue to protect and harden their nuclear sites, it will be more difficult to target and damage them. Both sides then discussed the upcoming delivery of bunker-busting bombs to Israel, noting that the transfer should be handled quietly to avoid any allegations that the US is helping Israel prepare for a strike against Iran."

The bombs duly arrived a few months later. The WikiLeaks cables also underpin a prediction made by western military officials earlier this year, that if Israel flew above Saudi Arabia to reach Iranian targets Saudi radar operators would somehow "fail to see them".

Yet Israel has hesitated. It is not the first time a year it deemed "crucial" has come and gone. Iran has now accumulated 3,000kg of low-enriched uranium – enough for two weapons, if further enriched. And this year Iranian scientists have stepped up the level of enrichment they are working on to 20%, which in terms of the technical obstacles that need to be overcome, is well on the way to 90% weapons-grade purity.

With each milestone passed, Iran has flaunted its achievements, yet Israel's sword has remained sheathed. It is clear that war is the last resort. Given diplomacy's ineffectiveness and the unknowable but terrible consequences of air strikes, it is easy to see why covert action is the least bad option; most of the successes and failures in this war will remain unsung, but some have made news.

In September last year, Barack Obama announced the discovery of a secret enrichment plant burrowed into a mountain near the city of Qom. It had been under satellite surveillance for some time. Western officials say that it was information from defectors and agents on the ground that confirmed the nature of the facility. Iran subsequently allowed IAEA inspectors into the site, but withheld blueprints which would have given away more of its ultimate purpose.

In June 2009, an Iranian nuclear scientist called Shahram Amiri disappeared while making the Hajj pilgrimage to Mecca. Three months later, the Iranian government claimed he was being held by the US – a claim echoed by several western reports that Amiri had defected and was living somewhere in America under a new identity. However, in July this year the scientist turned up at the Iranian interests section of the Pakistani embassy, claiming he had been held against his will and wanted to go home. Amiri returned to a hero's welcome in Iran, while back in the US he has been portrayed as a defector who lost his nerve.

Ahmadinejad admitted last week that Iran's uranium enrichment plant had been affected by the Stuxnet computer worm, which targeted the industrial management software that Iran uses to run its centrifuges. Like most computer viruses and worms, Stuxnet does not bear fingerprints, but a western military source recently told the Observer that it was an Israeli creation.

Ahmadinejad claimed that the damage caused by Stuxnet had been overcome, but the enrichment programme clearly has major problems that cannot be easily fixed. The IAEA reported last week that enrichment ceased altogether in mid-November. The centrifuges at the Natanz plant continued to spin, but no uranium gas was fed into them, a very rare stoppage that suggested there was a fault in the system.

The main centrifuge the Iranians are using, known as the P-1, is rudimentary and outdated and prone to crash, so that may be part of the problem.

But the US, Israel and other western spy agencies have also spent years slipping faulty parts into black market consignments of equipment heading to Iran – each designed to wreak havoc inside the delicate machinery requirement for enrichment.

Last week's events suggest that, as Iran continues to built up its stock of enriched uranium despite such difficulties, finesse is giving way to more brutal methods in this secret war.

Its first victim may have been Ardeshir Hassanpour, another top nuclear scientist, who co-founded Iran's nuclear technology centre in Isfahan. Officially, Hassanpour died from radiation poisoning in 2007. But some reports, yet to be confirmed, claimed he was killed by the Mossad. If that is true, the toll so far is three scientists dead, one wounded.

The front line in the war of Iran's nuclear project is not where most expected it to be drawn – at the enrichment plant in Natanz, or the mountain cavern at Qom, or the Revolutionary Guard bases where Iran tests its missiles. Instead it runs through university faculties and the leafy suburbs of north Tehran where Iran's academic elite make their homes. It is a covert war, with very high stakes, in which civilians are the primary targets, and Majid Shahriari is unlikely to be the last victim.