The leftist-nationalist prime minister will now need to find coalition partners to return for a third term.
Gains by small parties, including an extreme right one, may produce a divided parliament with no clear path to forming a majority government.
Robert Fico, 51, has vowed not to accept “one single Muslim” migrant.
Slovakia takes over the EU’s rotating presidency in July. His hard-line views on migration echo those of Polish, Czech and Hungarian leaders.
In all, nine parties, including the far-right Our Slovakia led by Marian Kotleba, will be represented in parliament. Our Slovakia won more than 8% of the vote.
With about 50% of the vote counted, Robert Fico’s Smer-Social Democracy party is on about 29% support, which would give it 48 seats in the 150-member parliament.
As the leader of the strongest party in Saturday’s poll, Robert Fico is expected to be asked to form a new government.
Robert Fico is known for populist policies such as free train travel for students and pensioners.
He has fiercely opposed EU quotas on migrant resettlement from Greece and Italy, which would see his country take about 2,600 people.
Slovakia received only 260 asylum requests in 2015.
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