The sources said they had recovered the bodies of 56 rebels, while six soldiers had been killed in the clash in the western Rolpa district, 460km west of Kathmandu, on Wednesday.
They also said 26 troops had been injured, seven seriously.
But Maoist sources claimed they had lost only seven cadres, although the toll was impossible to verify independently in the remote area.
Earlier officials said an army helicopter fired down on a base, believed to be used by senior Maoists before troops and police raided the complex from three sides.
An army official described the hideout as a “fortress” surrounded by sandbags and stones to protect it from attack.
It was the deadliest clash since the guerrillas ended a ceasefire last month.
The Rolpa district is where the Maoists declared their “people’s war” in February 1996.
Since then, the insurgency has claimed 8000 lives including 180 since the end of the truce, according to official figures.
The deaths came as life in Nepal was crippled as a three-day nationwide strike called by the Maoists got underway on Thursday.
They have been battling government forces since 1996, seeking changes in the constitution and an end to the country’s monarchy.