Adriano Nuvunga, director of Mozambique's Centre for Democracy and Human Rights, said that two journalists and a security guard were hit by bullets but not seriously wounded.
A police spokesperson could not immediately be reached for comment.
The full results of Mozambique's October 9 national election are expected this week, with early results showing that the ruling party Frelimo is set for another win.
Opposition candidates say the poll was rigged. Frelimo has ruled the southern African country since 1975.
Businesses closed
Mozambique's electoral commission has declined to comment on accusations of fraud.
"The police are turning this into a violent protest because they are firing at us. We are here to demand that the truth about the election is upheld," said protester Vladimir Manhique, a 32-year-old car mechanic.
Several hundred people took part in the protest, with some burning red Frelimo flags in the street and throwing rocks at the police.Independent presidential candidate Venancio Mondlane said that a national strike on Monday had been well observed and told the protesters to go home after the clashes with police. Many businesses were closed in Maputo and downtown streets were quiet.
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