"The first thing the new cabinet will investigate is the coup and conspiracy by president Rajapaksa," Mangala Samaraweera, a spokesman for the government led by President Maithripala Sirisena, told reporters here.
"He (Rajapaksa) stepped down only when the army chief and the police Inspector General refused to go along with him."
Rajapaksa, 69, was widely lauded for conceding defeat in the presidential election on Friday, even before the last votes had been counted.
Earlier, Rajitha Senaratne, the chief spokesman for the new president, said that Rajapaksa pressurised Army chief Lt Gen Daya Ratnayake to deploy troops after he lost election.
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"The army chief was under pressure to deploy but he did not. He declined to do anything illegal," said Senaratne.
"Even in the last hour, he tried to remain in office. Only when he realised that he had no other option, he decided to go," the spokesman said.
"We appreciate the straightforwardness of the Army Commander, Inspector General of Police and the Commissioner of Elections," Senaratne said.
There was no immediate comment from the military.
However, Rajapaksa's spokesman denied the claims as baseless.
"There was no such attempt at all," said Mohan Samaranayake.
"In fact, at 3:30 am on January 9 when the counting was still under way, the president made an assessment and decided what the results would be," he was quoted as saying by BBC.
"Then he gave instructions to all secretaries about a smooth transfer of power... The politician who has made these remarks is in the habit of making baseless allegations," he said.