Officials said the house was destroyed since they feared deadly booby traps, but rights activists and government critics said the move added to the mystery behind Maskhadov's suspicious killing.
Officials said last Tuesday that Maskhadov was killed during an operation by Russian forces in a basement bunker in the northern Chechen village of Tolstoy-Yurt, but gave few details of the operation.
General Arkady Yedelev, chief of the federal headquarters for the campaign in Chechnya, said demolition experts who inspected the bunker discovered and detonated a box that contained documents and was ridden with explosives.
"The team of investigators decided to blow up the entire house to avoid such surprises in the future," Yedelev said.
Federal troops arrived on Sunday in several trucks and armoured vehicles, ordered residents of neighbouring buildings to clear the area and then blew up the house, witnesses said.
A neighbour, who identified herself only by her first name, Zura, said the explosion shattered windows and cracked walls in her house. "It scared me and my children to death," she said.
While federal authorities said Maskhadov was hiding in the bunker, Yakha Yusupova - who lived in the house with her family - denied the rebel leader had been there and said she suspected Russian forces may have brought him on Tuesday.
Official version questioned
Anna Politkovskaya, a prominent Russian columnist and expert on Chechnya, said the house was apparently blown up to destroy any evidence that could cast doubt on official accounts of Maskhadov's killing.
"There is nothing left now to question the official version of events," Politkovskaya said in a telephone interview, scoffing at the official explanation.
"Can't they defuse booby traps without blowing up the entire house? she said.
Alexander Petrov of Human Rights Watch's Moscow office said federal authorities in the past had blown up houses in Chechnya that belonged to separatist fighters who participated in attacks.
The practice has drawn strong criticism from international rights groups, he said.
"If the authorities blew up the house to punish the house owners, it's a bad move," Petrov said.