Russian Health Minister Yuri Shevchenko lifted a veil of official secrecy about the gas following pressure from Western governments, whose citizens were among the hundreds of hostages poisoned by the gas.
Russia is now pressing Denmark to extradite Akhmed Zakayev, a senior official of the ousted Chechen Government detained in Copenhagen, whom it suspects of involvement in the mass hostage-taking.
Meanwhile, Russian troops are surrounding refugee camps along Chechnya's border as part of a military crackdown against suspected militants.
At least 119 civilians died in the storming of the theatre, where about 50 armed Chechens were holding almost 800 people hostage.
Of those rescued, 245 are still in hospital, eight in a serious condition.
Not lethal
There has been speculation that Russia's use of the gas may have violated the international Chemical Weapons Convention.
Fentanyl
Potent opium-based man-made narcotic
Used in medicine as pain killer
50 to 100 times more powerful than morphine
Not recommended for patients with liver problems, children or elderly
And Mr Shevchenko's statement came after a request for clarification about the gas from Rogelio Pfirter, director-general of the Organisation for the Prohibition of Chemical Weapons.
The minister stressed that the fentanyl gas, widely used in medical practice, "cannot in itself be called lethal".
He attributed the hostage deaths to the use of the chemical compound on people who were in a poor condition after three days of captivity - dehydrated, hungry, lacking oxygen and suffering acute stress.
"I officially declare that chemical substances of the kind banned under international conventions on chemical weapons were not used," he said, quoted by the Interfax news agency.
Earlier, the United States said more of the hostages might have survived if Russia had provided prompt information about the gas.
The lack of information "contributed to the confusion after the immediate operation to rescue the hostages was over," said Alexander Vershbow, the US ambassador to Moscow.
"It's clear that perhaps with a little more information at least a few more of the hostages may have survived," he said.
The rescue operation also left about 50 Chechen gunmen and women dead. They had held the hostages for three days.
Key Chechen detained
On the border between Chechnya and the republic of Ingushetia, Russian troops are taking position around refugee camps.
Almost 20,000 people live in the tent cities, after fleeing fighting in Chechnya over the past three years.
The BBC's Jonathan Charles says that in the aftermath of the Moscow siege, the Russian forces want to keep a much closer watch on the refugees.
But, our correspondent adds, the residents fear the Russian troops are about to carry out mass arrests.
Denmark, for its part, says it wants more evidence from Russia before it will agree to hand over Mr Zakayev, a senior envoy of Chechen President Aslan Maskhadov.
He was arrested in Copenhagen where he had been attending the World Chechen Congress - a gathering that had enraged Moscow.
Russia believes he was also involved in other "terrorist acts" between 1996 and 1999.
A Danish court ordered the detention of Mr Zakayev until 12 November.
"Russia should also promise that Zakayev would not receive the death penalty," the Danish Justice Minister, Lene Espersen, said.
Russia has had a moratorium on executions since 1996, but the death penalty has not been formally abolished.
Mr Zakayev's arrest came after police in Moscow detained 30 people, including security officials and political advisers, who are believed to have helped the Chechen rebels.