The move was the brainchild of Russian politicians who believed the amnesty, timed a month before the crucial elections in Chechnya, might erase anti-Russian sentiment in the region.
However, few had handed over the weapons when the Monday deadline arrived. The end of the amnesty coincided with the handover of control over public order from the FSB security to the Interior Ministry.
"September 1 marked the deadline for the guerrillas to give up weapons voluntarily," Deputy Prosecutor General, Sergei Fridinsky, told Interfax news agency.
The State Duma lower house approved the amnesty after an April referendum in Chechnya - boycotted by the rebels and criticised by human rights groups - showed a big majority voting to stay within Russia.
The poll, in which Chechens complained of being forced to vote through threats and intimidation, paved the way for Russia to organise 5 October election of a regional president.
The upcoming election is a key step in President Vladimir Putin's Chechnya peace plan which he hopes will put an end to the region's three years of de-facto independence.
The Chechen election is crucial to
Putin's ideas for subduing the region
Chechnya's Moscow-appointed administrator and a candidate in the October poll, Akhmad Kadyrov, has called for an extension of the amnesty.
His supporters say it would work in his favour during the campaign.
Moscow politicians also support an extension, saying it would stabilise the security situation and pre-empt attempts to disrupt the vote.
"It would work towards a trouble-free election," nationalities minister Vladimir Zorin told Itar-Tass news agency.
Russian officials say as many as 150 Chechen fighters have accepted the amnesty, but the military says about 3000 fighters continue to fight Russian rule in Chechnya – including 1000 hardliners.
Moscow admits, however, the numbers have remained unchanged in recent years despite daily losses inflicted on the rebels, as the separatists seem to have no difficulty finding new recruits.