Speaking at a news conference, Gayoom said: "This referendum was not about my leadership, it was about what form of government the people wanted to have in the future."
"But [with] this result, I am very much in position to say I am very happy with the endorsement, the massive endorsement that the people has given to our party position in the referendum."
He also rejected charges of vote-rigging from the opposition and called for cross-party unity.
Critics have said Gayoom is delaying the implementation of promised democratic reforms and say it is time he went.
Aides say he will run for office in the country's first multi-party election, due to take place next year.
Political parties were only legalised in the Maldives in 2005.
Gayoom's Dhivehi Rayyithunge Party's (DRP) and rival MDP accused each other of intimidating voters and breaking election rules.
"It comes as no surprise .... giving ballot boxes to election officials appointed by the president was like taking Dracula to the blood bank"
Mariya Didi, spokeswoman for the Maldivian Democratic Party
Election officials said ballot papers were short at some stations, and ordered a recount of one ballot box.
Mariya Didi, an MDP spokeswoman, said: "It is an ill-gotten result ... Look at how they used state media, bribery, corruption, voter intimidation and threats to withhold jobs.
"It comes as no surprise. The MDP always said giving ballot boxes to election officials appointed by the president was like taking Dracula to the blood bank."
Gayoom's critics say he is stalling on implementing a raft of democratic reforms pledged in late 2004 to revamp the power structure in the face of harsh criticism of the government's rights record.
His opponents billed a vote for a parliamentary system as a vote for him to quit, saying revenues from 89 luxury island resorts are not benefiting the half of the population who live in poverty on about a dollar a day.
Dissent has also flared within the ranks of Gayoom's cabinet.
Two members quit earlier this month, accusing him of stalling on a new constitution and judicial independence.