The elections on Wednesday were marred by rebel attacks, soldiers shooting protesters, low turnout and a boycott by most politicians to protest the king's absolute rule.
The elections were for the relatively powerless posts of mayor and local council member, and the dearth of voters at the polls was considered a more important indicator of popular sentiment than the election results themselves.
In initial returns on Thursday for 15 of the 36 cities and towns where polls were held, the pro-government Rashtriya Prajatantra Party won 10 mayoralties, the pro-government Nepal Sadbhawana won two and independent candidates won three, the Election Commission said.
Six people were killed in violence on election day, among them a protester shot by soldiers during the vote.
A coalition of the country's seven main political parties shunned the elections to protest the king's power grab just over a year ago, when he pledged to bring the country's Maoist insurgency under control.
However, rebel attacks continued, and have intensified in recent weeks.
"We refuse to accept the results from these so-called elections," said Krishna Sitaula of the Nepali Congress party, adding that those elected would be illegitimate.
"We will not accept them as representatives of the people and will not allow them to take their positions," he said.
Many voters said they were scared away from the polling by the Maoists' call for a general strike and their threats to kill anyone who took part and a government warning it would shoot anyone caught disrupting the elections.