Vote counting was under way in Mozambique on Thursday after a peaceful national election that is widely expected to see the ruling Frelimo party extend its 49 years in power.

Votes are counted first at each polling station and district results expected by Saturday could give an early indication of who is leading. Official results normally take around two weeks to be announced by the electoral commission.

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.

Frelimo candidate Daniel Chapo, 47, is likely to win. His party has been accused by opponents and election observers of rigging past elections, which it denies.

The manipulation of votes happens at many levels, from registering more people in Frelimo strongholds to appointing party loyalists to be polling station staff and changing the numbers at the end, said Joseph Hanlon, an advisor to civil society group Mais Integridade ("More Integrity").

A Frelimo spokesperson did not respond to questions from Reuters about alleged vote-rigging.

Election observer missions including the European Union's said that they had not recorded any major problems so far.

Chapo is a relatively new figure in national politics who would be the first president born after independence from Portugal in 1975. Analysts say he has the advantage of a clean record and distance from Frelimo's past corruption scandals.

His main challenger is Venancio Mondlane, an independent candidate who has fired up the country's youth. Former rebel commander Ossufo Momade and a small opposition party leader, Lutero Simango, are also competing to succeed President Filipe Nyusi, who is stepping down after serving the maximum two terms.