"This is the trend: Ikililou Dhoinine is leading, followed by Mohamed Said Fazul and Bianrifi Tarmidi," the minister of state in charge of the elections, Abderemane Ben Cheikh Achiraf, told AFP.
Official results from Sunday's poll are expected within 48 hours, according to Charcane Chaharane, an official with the electoral commission, but Achiraf ruled out any change in the trend.
Dhoinine is the ruling party candidate. Fazul is a former president of Moheli island and an opponent of the outgoing president Ahmed Abdallah Sambi.
Tarmidi is a former prime minister and another Sambi opponent.
In the governorship elections for Moheli island, which were held concurrently with the first round of the presidential poll, Mohamed Ali Said, the outgoing governor, was re-elected, the minister said.
Achiraf said the polls went well but he criticised what he called "the arbitrary arrests" of seven people on Sunday morning. All seven have since been freed.
The second round of the presidential poll will take place throughout the archipelago on December 26.