At least 15 protesters and two policemen were injured in Sebaco, around 90 kilometers from the capital.
Violence took place in some northern and eastern villages.
Ortega, a former leftist rebel and harsh critic of the United States, has changed rules to seek a third term against a weakened and divided opposition.
Polls put him ahead of his nearest rival with 40 per cent of the vote against 30 per cent for 79-year-old radio host Fabio Gadea.
With Ortega in the lead, his four right-wing rivals have focused on Congress, where 90 seats are up for grabs.
The 65-year-old ally of Venezuelan President Hugo Chavez helped overthrow the Somoza family dictatorship in 1979 and still heads the FSLN in Central America's poorest nation.
He claims he is continuing the 1980s revolution and still enjoys solid support in rural and marginalized areas of Nicaragua, where almost half of the population of 5.8 million live in poverty.
His opponents have slammed his bid to stay in power as well as the aid he has received from Chavez, estimated at over 1.1 billion euros since 2007, which has propped up popular social programs, including for subsidized housing.
The FSLN lost power in 1989, after a civil war against the US-backed Contra rebels. Ortega won a second five-year term as president in 2006.