Djukanovic's Democratic Socialist Party won the last general election in 2016, but he left the office to his deputy Dusko Markovic.
With 80 per cent of ballots counted, the Center for Monitoring and Research said on Sunday that Djukanovic had won about 53 per cent of the vote, ahead of his main opponent Mladen Bojanic with 34 per cent.
Montenegro's former prime minister and long-ruling Democratic Party of Socialists leader Milo Djukanovic speaks during a celebration after presidential elections in Montenegro's capital, Podgorica, on Sunday.
After the initial projections, party officials described the vote as a "great victory, a historic victory".
Founded in Montenegro are casting ballots in a presidential elections, with Prime Minister Milo Djukanovic expected to win following this past year, his celebration defied Russian Federation and required the modest Balkan state into North Atlantic Treaty Organisation.
The vote, the first since Montenegro joined North Atlantic Treaty Organisation in December, was seen as a test for Djukanovic, who favors European integration over closer ties to traditional ally Moscow.
"Milo Djukanovic is the new president of Montenegro", said Milos Nikolic, of the DPS.
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Djukanovic, the country's dominant politician, and his Democratic Party of Socialists have ruled Montenegro for almost 30 years. President Filip Vujanovic, also of the ruling party, was not running due to term limits.
Approximately 530,000 voters can choose among candidates.
Previously served as prime minister and once as a president, 56-year-old Djukanovic is returning to active politics after a brief break.
Montenegro's last parliamentary vote in 2016 was marred by the arrest of a group of Serb nationalists who had allegedly plotted to assassinate Djukanovic and bring pro-Russian parties to power, to stop the country's accession to North Atlantic Treaty Organisation.
He led Montenegro to independence from much-larger Serbia in 2006 and was behind the North Atlantic Treaty Organisation bid.
"I understand this election result as a confirmation of Montenegro's evolution to achieve European values, European standards and full membership in the European Union", Djukanovic said before opening a bottle of champagne. Opposition member Mladen Bojanic came second. The Kremlin has denied involvement.