One person was killed by police dispersing a crowd at a voting station after the polls had closed in the northern port city of Nacala, according to local reports.
Leading opposition figures had urged their supporters to stay and monitor the vote counting, despite official announcements that only accredited observers and polling station staff could remain at the premises after hours.
Another crowd refused to leave a polling station in Maniamba, in northern Niassa province, leading to a scuffle with police in which ballot papers were destroyed, according to local radio reports.
Pre-marked ballot papers were discovered in several incidents up and down the country, according to the civic group, the Center for Public Integrity. In all cases the ballots were marked in favor of the ruling Frelimo party, it said.
A senior opposition politician, Renamo's national spokesman Jose Manteigas, was arrested in Inhambane, in southern Mozambique, in an apparent dispute over his accreditation to observe the voting process, according to local reports.
Results could take days to be announced. The National Election Commission will not release partial results during the counting process as it had done in the past, said commission head Sheik Abdul Carimo, according to the newspaper, Canal de Mocambique.
In the previous elections in 2014, the election commission held press conferences every few hours to announce the results as they came in. The commission decided announcing preliminary results in this election, Carimo said, because they "can create various negative interpretations."