He said William McNeilly's allegations were either factually incorrect or the result of misunderstanding or partial understanding.
The Royal Navy submariner has claimed missile programme system on the Clyde was a "disaster waiting to happen".
He wrote a report, detailing "serious security and safety breaches".
In a statement addressing the 25-year-old's concerns, Mr Fallon insisted that neither the "operational effectiveness" of the fleet "nor the safety of our submariners or public have been compromised".

Most of the churches affected had predominantly African-American congregations.
"We believe that this fire-setting activity is meant to send a message," said John Ham of the Bureau of Alcohol, Tobacco, Firearms and Explosives.
The most recent fire broke out early on Thursday morning.
"It was really disheartening to see what you worked so hard for brought down in a matter of minutes," said Pastor David Triggs of the United Believers in Christ Church, which was heavily damaged on 17 October.
The fires have all been set at the front or side doors of buildings, usually without causing serious structural damage.
This was not the case for Pastor Triggs, who said his church's building is likely unsalvageable.
That leaves his roughly 70 active congregants without a house of worship.
He is holding services on the lawn this coming Sunday while trying to determine next steps.
"We're kind of at a cross road," he said. "I have no doubt that God is going to provide for us."

The attack took place at about 06:00 in the northern town of Kidal. Residents said at least two suicide bombers were involved and a car bomb was detonated.
A soldier from Chad was killed and at least one other was injured.
A 9,000-strong UN force has been responsible for peacekeeping operations in Mali since July 2013. It regularly comes under attack from militants.
An official from the UN force, known as Minusma, confirmed the attack to Reuters news agency, but did not provide further details.
French and African troops intervened in Mali in January 2013 to stop the southern advance of al-Qaeda-linked fighters on the capital, Bamako.
The insurgents were expelled from the northern towns but have continued attacks against Minusma, which took over responsibility for security in the country from the French.
The UK's Defence Secretary Michael Fallon has said a whistleblower's concerns about Trident nuclear submarine safety have not been proved.
[NEXT_CONCEPT]
Police in the US state of Missouri are searching for arsonist who set fire to seven churches in the St Louis area in the past two weeks.
[NEXT_CONCEPT]
Gunmen have launched an attack on a UN camp in Mali, killing a UN peacekeeper, residents and eyewitnesses say.