With 100 per cent of the ballots counted after Monday's election, Guterres secured 57 per cent of the vote, according to figures from the Technical Secretariat for Electoral Administration which were released on Wednesday.
His closest rival, social affairs and education minister Antonio da Conceicao, was in second position with 32.5 per cent.
Guterres will be the first presidential candidate to have won a clear majority in the first round since independence hero Xanana Gusmao was overwhelmingly elected as president in 2002.
The result is expected to be confirmed on April 2.
Guterres is backed by the Fretilin party and CNRT, the party founded by Gusmao, who provided key support to Guterres during his election campaign.
The election was the first since United Nations peacekeepers left the country in 2012.
Analysts said the outcome of the election is likely to strengthen stability in the tiny nation of 1.2 million people.
Supporters of Presidential Candidate from Fretilin party Francisco Guterres Lu'Olo shout slogans as Guterres arrives at Fretilin's headquarter in Dili. Source: EPA
East Timor's economy is heavily reliant on oil revenues but its $US16-billion sovereign wealth fund derived from petroleum money is fast drying up, analysts said.
The country remains one of the world's poorest, with about 40 per cent of its population categorised as poor.
Violence erupted after East Timor voted for independence from Indonesia in a UN-sponsored vote in 1999 as Indonesian troops and pro-Jakarta militia unleashed a campaign of destruction.
The United Nations administered the former Portuguese colony until 2002, when it became formally independent, but a UN mission stayed until 2005 to help the fledgling country establish state and security institutions.
A UN peacekeeping mission was deployed in 2006 after a new bout of political violence.
Timor Leste election
Early count puts Francisco Guterres ahead in Timor-Leste election
