Political tensions have soared since protests against a now-aborted pension reform began on April 18 and mushroomed into general opposition to President Daniel Ortega and his government.
Friday's attacks came as Ortega called for peace during a day of strikes, the second in three months of anti-government protests that have left over 270 dead.
Two people were killed when government forces opened fire on the combative neighborhood of Monimbo, south Masaya, as Ortega and his supporters began a procession from the capital to the opposition stronghold, 30 kilometers (19 miles) south. One was a policeman, a local rights group representative told AFP.
The march was to celebrate the June 1979 "retreat" that saw thousands of guerrillas withdraw from Managua to Masaya to regroup, before securing victory on July 19 when president Anastasio Somoza fled the country.
On Friday, protesters erected barricades and vowed to prevent the former leftist guerrillas procession from passing through. It was delayed and limited to a driven caravan.
But where Ortega was once hunkered down with allies in Masaya fighting against a dictatorship, the 72-year-old head of state now is now the one hated in the rebel heartland.
In Masaya, Ortega accused the opposition of acting "with venom and hate," and appealed for a return to "the road of peace."
Elsewhere at the National Autonomous University of Nicaragua, where students have been holed up since protests began, a medic reported several injuries after pro-government forces opened fire.
"They all came with firearms, they came to kill," one young person told reporters from a church near the university.
- Second strike -
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Meanwhile, banks, markets, gas stations, schools and shops kept their doors locked among deserted streets as Nicaragua's opposition staged a 24-hour general strike on Friday, a day after five people were killed in violence surrounding anti-government protests.
Opposition supporters claimed the strike was 90 percent respected across the country while official media announced business as usual in several trade zones.
In cities such as Leon and Granada, only state-owned Petronic gas stations remained open.
Mercado Oriental, one of the biggest trade centers in the capital Managua with 20,000 businesses, was almost entirely shuttered.
"I'm working out of necessity but the strike is a weapon to put pressure on the government because there is no end in sight to this situation," Adolfo Diaz, a 67-year-old shoe shiner, told AFP while sitting alone in a hall at the Huembes market in the east of Managua, normally a bustling hub of some 4,500 businesses.
The strike, called by the opposition Civic Alliance for Justice and Democracy grouping, came after four police officers and a protester died on Thursday as clashes erupted between opposition activists and government forces and their paramilitary allies in the southeast town of Morrito.
- 'Terrorist' arrested -
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On Friday, police arrested opposition leader Medardo Mairena, accusing him of being a "terrorist" and having "organized" and "ordered" the "attack" against the murdered police and protester.
The opposition Civic Alliance denounced Mairena's detention as an "act of intimidation."
The opposition is demanding either early elections or the resignation of Ortega and his wife Vice President Rosario Murillo, accusing both of corruption, despotism and nepotism.
But while the will was there to support the strike, not everyone has the means to do so.
"If I don't work, I don't eat. It's not a question of not supporting the strike but one of supporting our families. We need this to end so we can work," said 56-year-old cobbler Nestor Larios.
The strike is part of three days of nationwide protests against the government that began on Thursday with a sea of blue and white clad demonstrators marching through Managua and is due to end with a car caravan through flashpoint areas of the capital on Saturday.
Police have blamed the violence on "terrorist groups" that pretended to be carrying out a peaceful march and opened fire on a police station.
Protesters also abducted nine police officers and attacked the Morrito town hall, the police said in a statement.