Gjorgje Ivanov will contest a run-off against Ljubomir Frckoski on 5 April
The candidate of Macedonia's governing conservatives has emerged as favourite for the presidency after a first-round vote praised for its lack of violence.
With nearly all votes counted, Gjorgje Ivanov of the VMRO-DPMNE party leads with 35%, followed by the Social Democrats' Ljubomir Frckoski on 20%.
The two candidates will face each other in a second round run-off on 5 April.
Earlier, the EU's envoy praised the "calm and positive atmosphere" of Sunday's presidential and local polls.
"It seems that everything was in order," Erwan Fouere told reporters.
A peaceful vote was seen as crucial for Macedonia's drive to join the EU and Nato, after gun battles between rival ethnic Albanian parties marred last year's parliamentary election.
A long-running dispute with Greece over Macedonia's name has also threatened the former Yugoslav republic's EU and Nato bids.
A total of seven candidates stood to replace President Branko Crvenkovski, who did not seek a second five-year term in the largely ceremonial post.
With ballots counted from 95% of polling stations, Mr Ivanov - the candidate of Prime Minister Nikola Gruevski's VMRO-DPMNE party - had established a clear lead with 35.06%, the election commission said.
He was followed by Ljubomir Frckoski, who is backed by the main opposition Social Democratic Alliance of Macedonia (SDSM), on 20.45%.
Trailing them were former Interior Minister Ljube Boskoski, who was acquitted by the UN war crimes tribunal in The Hague last year, and ethnic Albanian leader Imer Selmani.
After the vote, Mr Ivanov said Macedonia's people had "proved that we have capacity to conduct fair and democratic elections".
"We have proved that European values live in Macedonia and that this country deserves to become an equal member of the EU and Nato," he added, calling for a strong turnout in the second round.
Prime Minister Nikola Gruevski, leader of the VMRO-DPMNE, hailed the vote as "one of the most successful" in Macedonia since independence in 1991.
Ljubomir Frckoski is backed by the main opposition party, the SDSM
But opposition parties complained of irregularities, including voter intimidation. The SDSM said the election had been "far from fair".
"We have had a day free of violence," SDSM spokesman Gjuner Ismail said. "But people were frightened by governing party supporters."
More than 500 international and around 7,000 local observers were on hand to monitor Sunday's vote.
The Organisation for Security and Co-operation in Europe (OSCE) will give its verdict on the conduct of the poll later on Monday, after which the electoral commission is expected to confirm the results.
Results from the local elections also held on Sunday meanwhile showed the VMRO-DPMNE party comfortably ahead, winning 18 of the 85 mayoral posts outright, compared with just three for the SDSM.
Heavy snowfall had prevented 134 of almost 3,000 polling stations from opening on Sunday, but the electoral commission said the affected polling stations had 12,556 voters registered - less than 1% of the total 1.8 million eligible voters.
Heavy snowfall disrupted the vote in a minority of districts
The three weeks of campaigning passed off mostly peacefully, with a few claims of voter intimidation.
One person was killed and several injured in ethnic Albanian areas of Macedonia during parliamentary elections in June 2008 that monitors said fell short of international standards.
Mr Fouere said the vote was "the last chance not to miss the train again to EU" membership.
"This is probably the last opportunity for quite some time for the country to show that it has not only the capacity, but also the political will, to organise elections in line with international standards," the EU envoy said.
Last year, Greece said it would block Macedonia from joining Nato and the EU unless it compromised over its official name. Macedonia is also the name of a northern region of Greece.
In December 2008, Macedonia decided to take the issue of its name to the International Court of Justice in The Hague.