A low referendum turnout could complicate his task of persuading more lawmakers that the name change enjoys popular support. He halted the construction projects of the previous government, and changed the name of the airport and the highway.
Under the deal, Greece would drop its complaints.
Just 36.5 percent of eligible voters turned out on Sunday (30 September) to answer the question: "Are you for European Union and North Atlantic Treaty Organisation membership by accepting the agreement between the Republic of Macedonia and the Republic of Greece?".
Reactions to the vote were mixed in Greece, where the government has faced pressure from nationalists over the deal. They seized on Sunday's low turnout as evidence of the agreement's rejection. However, barely 300 people gathered there an hour and a half after the polls closed. The figure was based on data from 85 percent of polling stations.
Christian Mickoski, the leader of the main opposition VMRO-DPMNE party, said the strongest message in the referendum was sent by those who boycotted or voted against the deal with Greece.
Macedonian Prime Minister and SDSM party leader Zoran Zaev said the issue would now be moved to parliament, and if that does not succeed, he announced early parliamentary elections. It would have helped him win parliamentary support for the required constitutional amendments to move forward.
He said he would call snap elections as early as November if he failed to muster the two-thirds vote in parliament needed to implement the deal. A poll in June shows most Greeks oppose the deal.
Macedonian President Gjorge Ivanov slammed the deal as a "flagrant violation of sovereignty".
Voters in Macedonia took to the polls on Sunday to decide on a controversial referendum on whether to change the name of their country - a move that would pave the way for entry into North Atlantic Treaty Organisation and the European Union.
When Macedonia declared independence during the break-up of Yugoslavia in 1991, Greece objected to its new neighbour's name.
Although the two governments promote the deal, there are still many people in both countries opposing the agreement.
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"Part of the population is concerned that the change of name will change certain identity markers, even though our nationality and language will be recognised as Macedonian", said Prof Kacarska, who gained her PhD at Leeds University.
"This is good news for those opposed to the agreement (as Macedonia Prime Minister Zoran) Zaev was seriously hurt in the (referendum) process", Angelos Syrigos, a professor of global law at Panteio University, wrote in Ta Nea daily.
Zaev cast his ballot in the southeastern town of Strumica and called on his fellow citizens to ensure a strong turnout.
The referendum is non-binding, allowing the government to take the outcome as a fair reflection of public opinion regardless of the turnout.
For nearly 1.8 million Macedonians polling stations will be open from 7 am to 19 PM local time.
Macedonia should "continue to implement this agreement", Greek leader Alexis Tsipras told Zaev by phone after the result came out. It is ratified by the Macedonian parliament in July and, if accepted in Sunday's referendum, will need to go back to parliament which must approve constitutional changes.
"I came today to vote for the future of the country and for young people in Macedonia".
Zaev said Macedonians "are deciding the fate of our country".
Macedonia's prime minister pledged yesterday to press on with a vote in parliament to change the country's name to resolve a decades-old dispute with Greece, despite failing to secure the 50 per cent turnout at a referendum required to make it valid.
The following month they open liaison offices in their respective capitals and a new Macedonian flag - with the controversial rayed sun replaced - is raised for the first time at the United Nations. Greeks, who consider this one of the high points of their history, see the use of the name by their northern neighbor as an attempt to usurp their history.