Assoumani has been ruling the Indian Ocean archipelago nation since 1999 when he first came to power through a coup.
Since then, he has won three elections. Critics accuse his government of cracking down on dissent, which it denies.
Results published by the national electoral commission late Tuesday showed Assoumani garnered 62.97% of the vote.
The country of about 800,000 people has experienced around 20 coups or attempted coups since winning independence from France in 1975 and is a major source of irregular migration to the nearby French island of Mayotte.
"We can not talk about results because there was no election," Mouigni Baraka Said Soilihi, one of Assoumani's opponents, said after the results were published, adding the election had been tainted by irregularities including closing polls before the legally prescribed time.
On Sunday, other opposition leaders said there were instances of ballot stuffing. They had called for a boycott of the poll, accusing the election commission of favouring the ruling party. The commission denies the charges.
Houmed Msaidie, Assoumani's campaign director, also denied the allegations and asked the accusers to provide evidence.
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