Votes were being counted by Mozambique's national election authorities on Thursday as civil society monitors were compiling a parallel tally to try to detect possible signs of fraud.

The Southern African country voted on Wednesday in a national election that is widely expected to see the ruling Frelimo party extend its 49 years in power. Frelimo has been consistently accused of rigging elections, which it denies.

Some observer missions noted issues with preliminary vote counting that took place overnight. More than 200 polling stations denied journalists and observers access to the process, said Sala da Paz ("Peace Room"), a civil society platform.

"There were significant cases of .... electoral irregularities that may raise questions about the credibility of the process," it said in a statement.

Mozambique's National Election Commission did not immediately respond to a request for comment.

In a makeshift data lab at the Centre for Public Integrity in the capital Maputo, staff uploaded pictures of handwritten results sheets from polling stations sent in by their observers. An app they created pulls the data and crunches the numbers.

"This is very important (because) historically speaking, the electoral process in Mozambique is characterised by fraud," said Analgencio Makamo, a data analyst for the observer mission Mais Integridade ("More Integrity").

The electoral commission is expected to release its first preliminary results on Saturday, with full results not expected for two weeks. Past elections have shown significant discrepancies between the official and parallel counts.

Four candidates are vying to replace President Filipe Nyusi, who has served the maximum two terms. Frelimo has put forward Daniel Chapo, 47, a former governor and law professor.

His main challenger is Venancio Mondlane, an independent candidate who has fired up the country's youth.

Analysts expect isolated protests if the outcome is disputed.

"Everybody here hopes Venancio will win. It's going to be chaos if he doesn't," said Siaca Chemuna, 42, a resident of Maputo's working-class Mafalala neighbourhood, where red flags saying "Vote Frelimo" flew over tin-roofed shacks.

The winner will inherit an Islamist insurgency in the north that has halted multi-billion dollar gas projects and displaced hundreds of thousands of people. Other challenges include high debt levels and the economic impact of worsening cyclones.

Helena Cossa, a 25-year-old entrepreneur, said she hoped her vote would count.

"We are going to wait for the results but I don't think the elections were free," she said.