The June deal would pave the way for North Atlantic Treaty Organisation and possibly European Union membership, ending a dispute dating from the early 1990s when Macedonia declared independence from Yugoslavia.
Macedonia's PM Zoran Zaev gives a speach during a referendum night on changing Macedonia's name that would open the way for it to join North Atlantic Treaty Organisation and the European Union in Skopje, Macedonia September 30, 2018.
Greek Prime Minister Alexis Tsipras expressed his support for his Macedonian counterpart in a telephone call in which he hailed the "determination and courage" of Zoran Zaev to "complete the implementation of this agreement", a government source told AFP.
The Macedonian Constitution requires a minimum turnout of 50% of eligible voters for a binding referendum.
"MPs now have an obligation to make Macedonia a better place for all of us", Zaev told reporters late on Sunday.
"The government has lost its legitimacy, and the only thing remaining is to respect the will of the people", Hristijan Mickoski, leader of the main center-right opposition party, VMRO-DPMNE, wrote on Facebook.
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A poll published last Monday by Macedonia's Institute for Policy Research (IPIS) said between 30 and 43 percent of voters would take part in the referendum - below the required turnout.
Macedonia proclaims its independence from Yugoslavia in 1991 but its worldwide recognition is immediately stalled by Greece because of its name.
The prime minister of Macedonia has declared a referendum on changing the country's name a "success for democracy and for a European Macedonia", and plans to address citizens again once results and final turnout figures are in. "I now expect all political leaders to respect this decision and take it forward with utmost responsibility and unity across party lines, in the interest of the country". Zaev said that if opposition parties did not support the constitutional changes, then he would resort to "another democratic tool" - a call for early elections as soon as November - to ensure that the changes would be made.
For decades Greece and the former Yugoslav Republic of Macedonia (FYROM) had a contentious relationship over the name. The dispute stretches back almost three decades, with both countries claiming links to Alexander the Great's ancient empire of Macedon, which spanned the territories.
Zaev is billing the vote as a painful but historic opportunity to break the 27-year-old stalemate.
Opponents in Macedonia have called for a boycott of Sunday's referendum and include the country's president, Gjorge Ivanov, who calls the deal a "flagrant violation of sovereignty".
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The DIK also announced that of those same 98.61 per cent of votes counted, 91.48 per cent of votes were in favour of the deal with Greece, and 5.64 per cent were against.
But a desire to anchor their future to the West - and the economic prosperity that it could bring - has been a driving force behind the "yes" vote in one of Europe's poorest nations.
The referendum was non-binding, but its failure will make it hard for him to get the two-thirds majority he would need to get it through.
"We urge leaders to rise above partisan politics and seize this historic opportunity to secure a brighter future for the country as a full participant in Western institutions", U.S. State Department spokesperson Heather Nauert said.
"Macedonia has spoken today - Macedonia said - the deal is off".
While Macedonia avoided the full-scale inter-ethnic wars that rippled across the region during the collapse of Yugoslavia, it was roiled by an Albanian insurgency in 2001 that left more than 100 dead. Similarly, Stoltenberg said: "We have seen Russian Federation trying to interfere in democratic political processes in this region for many years".
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In response, prominent Western figures, including the USA secretary of defense, Jim Mattis, visited Macedonia to try to persuade voters to back the name change.