The ruling Sandinista Front has won at least 134 of the 153 mayoral races in local elections the opposition and the U.S. government say lacked transparency, according to results released Monday.
At least three people have died and dozens more have been injured in clashes between rival political groups since Sunday's elections, authorities said.
Police Commissioner Fernando Borge said two people died in Ciudad Dario, about 28 miles (45 kilometers) north of the capital.
Octavio Alvarez, Sandinista Front's political secretary, said a member of the Sandinista Youth was shot to dead in the town of Nuevo Segovia.
With more than 91 percent of the Sunday vote counted, the Sandinistas had 76 percent of the vote, said Roberto Rivas, president of Nicaragua's Supreme Electoral Council.
Led by President Daniel Ortega, who was re-elected for another five-year term last year, the Sandinistas have made major advances in municipal elections. The party currently governs 109 municipalities, including the capital, Managua, where journalist Daysi Torres was re-elected.
But the opposition argues there was widespread fraud and the U.S. government said it was concerned the elections were not fully transparent, echoing claims made during local elections four years ago.
"We do not believe in the results given by a completely discredited Electoral Council, with no credibility and that plays on the side of (the Sandinistas), and that allows dead people to be listed as candidates," said Congressman Eliseo Nunez, of the opposition Independent Liberal Party, referring to reports that in several cities in northern and central Nicaragua there were people listed as candidates who had died or live abroad.
"We participated because the people should have a choice," Nunez added. "But we know that everything was rigged and the Electoral Council did what Daniel Ortega ordered."
In the town of La Paz Centro, supporters of the Sandinista Front and those of the Liberal Independent Party fought each other and anti-riot police with stones, tear gas and rubber bullets.
"Opponents do not know how to lose. They have burned and destroyed public buildings in acts of vandalism that must be punished," said Lesbia Abarca, mayor of the town located 35 miles (56 kilometers) west of Managua.
Before polling stations opened on Sunday, the opposition denounced the voting lists were confusing and had been altered. They also claimed supporters of the Sandinista Front were allowed to vote twice.
The U.S. State Department in a statement expressed concern that the elections "failed to demonstrate a degree of transparency that would assure Nicaraguans and the international community that the process faithfully reflected the will of the Nicaraguan people."
Irregularities observed on election day included citizens being denied the right to vote, a failure to respect the secrecy of citizens' votes, and reported cases of voters being allowed to vote multiple times, it said.
"These disturbing practices have marred multiple recent Nicaraguan elections," it added.
After the 2008 municipal elections in Nicaragua, the U.S. suspended some $64 million in development aid because of the fraud allegations.