Defense Minister Javier Zabaleta said a "police mutiny occurred in a few regions," but he rejected the idea of a military intervention "at this time."
The disputed results of the Oct. 20 election have triggered a wave of protests across Bolivia, which have resulted in three deaths dead and more than 300 injuries.
Earlier in the day, opposition leader Luis Fernando Camacho vowed not to leave the capital of La Paz until Morales personally accepts a resignation letter drafted for him. At a separate public event, Morales repeated that he is not resigning
In the evening, a small group of police officers staged a rebellion in the central Bolivian city of Cochabamba, apparently demanding the resignation of their commander, who has been accused of siding with Morales' supporters during clashes this week that left one person dead and more than 100 injured.
Television stations broadcast images of the 18 police officers standing on the roof of the special operations tactical unit in Cochabamba, waving flags and singing the national anthem as a large crowd of people in the street cheered.
Hundreds of residents in other cities clamored outside local police stations urging officers to "follow their example." Police in Santa Cruz, an opposition stronghold, affixed a sign on their station saying they were revolting. Police officers in other cities left the streets and returned to their stations, without explaining why.
Morales convened an emergency meeting with his ministers and military high command to analyze the situation.
"There is no order. There will be no military operation at this time. It's discarded," Zabaleta said following the meeting.
Gen. Yuri Calderón, head of the national police, had previously denied that a police rebellion was under way and called the Cochabamba incident "isolated."
"There is normalcy in the rest of the country and we hope that services will resume," he said.
Later, the government later denounced what it called "an attempted coup," accusing the opposition of plotting to oust Morales.
Morales declared himself the outright winner even before official results indicated he obtained just enough support to avoid a runoff with former President Carlos Mesa. But a 24-hour lapse in releasing vote results fueled allegations of fraud by the opposition.
The Organization of American States is conducting an audit of the election count and their findings are expected Monday or Tuesday. The opposition says it will not accept the results because they were not consulted on how the process would unfold.
Protests have been most intense in La Paz, Potosí and Santa Cruz, that latter an opposition stronghold where Camacho, president of the Pro Santa Cruz Civic Committee, is based.
On Thursday in La Paz, members of the tourism sector marched in the middle of an anti-Morales demonstration holding white balloons and urging calm.
"We are asking for peace. We don't have a position in favor or against. We are asking that both sides hear us," Sergio Rengel, a leader in the tourism sector, told The Associated Press. "It's been 17 days in which we've been losing about $5 million a day."
Morales' bid for re-election was controversial before it began. The former union leader, and Bolivia's first indigenous president, has shepherded significant economic growth and an overhaul of the constitution. But he refused to accept the results of a referendum upholding term limits. The country's constitutional court later ruled that term limits violated his human right to run for office, and the electoral court ultimately accepted his candidacy for a fourth term.