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.
Source: Reuters