Syriza took 26.7 percent of the vote, ahead of the conservative New Democracy which took 22.8 percent, according to the official projection by the interior ministry. The projection has a margin of error of 1 percentage point.
The co-ruling Socialist PASOK party's Olive alliance secured 8.1 percent of the vote, while the far-right Golden Dawn placed third with 9.3 percent of the vote.
The EU ballot marks the first major electoral test for Samaras since he came to power two years ago and has turned into a de facto referendum for his fragile right-left coalition, which is clinging to a two-seat majority in parliament.