"The trigger man will be blamed, while those who actually ordered the killing will go free," Ilya Yashin, co-founder of Mr Nemtsov's party, said on Sunday.
His comments came after two men of Chechen origin were charged with his murder and three others arrested.
Mr Yashin rejected suggestions radical Islamists were behind the murder.
"The investigators' nonsensical theory about Islamist motives in the killing suits the Kremlin and takes [President] Putin out of the firing line," Mr Yashin said on Twitter (in Russian).
Those behind the killing were in Russia and even in government, he said separately in a BBC interview.
On Sunday, a court in Moscow charged Zaur Dadayev and Anzor Gubashev with shooting Mr Nemtsov on a bridge near the Kremlin on 27 January. Mr Dadayev had admitted his involvement, the court said.
Three other suspects were remanded in custody. A sixth man was reported to have killed himself in a standoff with police in the Chechen capital Grozny.
Chechen leader Ramzan Kadyrov, an ally of President Vladimir Putin, described Mr Dadayev as a devout Muslim who was shocked by cartoons of the Prophet Muhammad published in French satirical magazine Charlie Hebdo.
"All who know Zaur [Dadayev] confirm that he is a deep believer and also that he, like all Muslims, was shocked by the activities of Charlie and comments in support of printing the cartoons."
Along with other Russian politicians and activists, Mr Nemtsov had condemned the killing of 12 journalists at the French satirical magazine by Islamist extremists.
But he also criticised threats made by the Chechen leader towards those who did not condemn cartoons published by the magazine.
Mr Kadyrov had declared former oil tycoon Mikhail Khodorkovsky his "personal enemy" for urging other papers to republish the Charlie Hebdo cartoons.
He had also said Ekho Mosvky editor-in-chief Alexei Venediktov "would be called to account" after his station's website ran a poll on whether media should publish similar cartoons.
This prompted Mr Nemtsov to accuse Mr Kadyrov of violating Russia's criminal code by infringing journalists' activities.
"Everybody is already sick and tired of Ramzan's threats, but he is certain that [President] Putin will not let anyone touch him, so he is growing increasingly brazen every day," Mr Nemtsov wrote on his Facebook page in January.
Mr Kadyrov received a medal of honour from President Putin on Monday. The award was for "his outstanding achievements, social activities and many years of honest work," a presidential decree said.
Mr Yashin told the BBC that Mr Nemtsov had not been a prominent critic of radical Islam and had concentrated his attacks on President Putin and his government.
He said he did not believe Mr Nemtsov's killers were from outside Russia, calling his murder "an act of terror to scare society".
If the Russian authorities had any proof that the two men charged were the killers, that proof should be made public, he said.
"I believe that the organisers of the murder are in Russia and I believe that they are in the Russian government," he added.
The location of the murder, right next to the Kremlin, made him think that the killers could not have acted without support from the authorities, he said.
He said people criticised by Mr Nemtsov in recent years should be under investigation.
Mr Nemtsov's daughter, Zhanna, also said she was convinced her father's critical views of the Kremlin were the reason behind his death.
Appearing on a talkshow on German television on Sunday evening, she said the Kremlin would have had a motive to kill him.
"My father wanted to convince the West that those at the top of Russian television were lying to the public," she said, adding that if those now arrested effectively worked for the Chechen interior ministry, "the political responsibility did indeed lie with the government in Moscow".
The three men remanded in custody are Mr Gubashev's younger brother, Shagid, and two men named as Ramzan Bakhayev and Tamerlan Eskerkhanov. Reports say all three have denied any involvement in the murder.
The Russian Investigations Committee is treating the case as a "contract killing", Interfax news agency reported.
President Putin has condemned Mr Nemtsov's murder and called for an end to "shameful" political killings in Russia.
Mr Nemtsov was killed days before a march he had been organising against the conflict in Ukraine.
He had also been drafting a report expected to expose covert Russian military involvement in the conflict.
A close ally of murdered Russian opposition politician Boris Nemtsov says he is "totally sceptical" that the two men charged organised his killing.