Independent election observers, including former U.S. President Jimmy Carter, said the elections were fair, honest and free of any irregularities.
Carter met Maoist leader Pushpa Kamal Dahal late Thursday to urge him to drop the boycott, accept the results and take part in the elected Constituent Assembly.
Government and election officials have rejected the party's claims.
Final results from Tuesday's vote to elect 601 assembly members are not expected until late next week, as ballot boxes were still being transported by helicopters and even on foot by porters to counting centers in the mountainous country.
The Maoists are former communist rebels who fought government troops between 1996 and 2006. They gave up their armed revolt, joined a peace process and mainstream politics, and their fighters have joined the national army.
Political leaders in the last assembly elected in 2008 disagreed over who got to lead the nation and on creating a federal system divided by ethnic groups or by geography. The resulting power vacuum has left Nepal without a proper constitution.