"This is horrible. You can't live in peace anymore, people are dying because of a government that won't leave," 40-year-old housewife Ramona Aleman told AFP at the cemetery in the north of the city, as a victim of Tuesday's violence was laid to rest.
Marvin Lopez was shot in the throat and his friend Edgar Taleno said he and his friends had to dodge gunfire from pro-government forces to retrieve his body.
"This is total anarchy. We ask the international community to support us. We can no longer live here, they are massacring people who don't have weapons," Taleno said.
Riot police and paramilitaries had deployed Tuesday in the historically combative city, dressed in black and wearing balaclavas, after it declared itself in rebellion against Ortega's government.
Riot police entered the city to leave munitions and food for the police, and removed some barricades. Police in the city are remaining in their barracks. But according to a priest in the Monimbo neighborhood, Augusto Gutierrez, the opposition remain in control of some areas of the city.
The pro-Ortega forces used tractors and tow trucks brought in from the capital Managua to clear barricades from the main road leading to the city.
Anti-government protesters erected new barricades in some neighborhoods overnight, as witnesses said trucks carrying armed men patrolled the streets of the city, 35 kilometers (22 miles) south of Managua.
Ortega's wife and vice-president, Rosario Murillo, said her husband "is committed to curbing this wave of terrorism, hate crimes, kidnappings, threats and intimidation."
Elsewhere, residents in the towns of Jinotepe, Leon, Matagalpa and Esteli reported shootings and attacks by heavily armed men.
"There are situations of extreme violence where they are already exceeding the limits, and the truth is that we find ourselves totally defenseless," the executive director of the Nicaraguan Center for Human Rights, Marlin Sierra told AFP.
"The tendency is to deepen the crisis," said Sierra. "We are extremely worried because we see that there is a political will on the part of the state to push for a civil war."
On Tuesday, the rights group's head Alvaro Leiva said residents were resisting "within the scope of their possibilities" but were under "disproportionate" attack by security forces.
The auxiliary bishop of Managua, Silvio Baez, appealed to the government to back off.
"Stop the attack on Masaya. Respect the life of the population," he tweeted.
The country's Roman Catholic bishops have attempted to mediate the crisis. But the latest attempt collapsed on Monday, with the bishops and opposition accusing the government of failing to act on a promise to allow international organizations to investigate the violence.
Masaya, once a bastion of Ortega's Sandinista revolution, has been a focal point of protests aimed at forcing him out of office.
A onetime leftist guerrilla, Ortega led the country from 1979 to 1990 and then returned to the presidency in 2007.