Maliki's State of Law coalition, an alliance of his Dawa party and some Sunni tribal leaders, Shi'ite Kurds, Christians and independents, led in Baghdad, the biggest electoral prize with about 8 million people, according to informal tallies.
State of Law was the big winner in January 2009 provincial elections and campaigned on a platform of improved security and strong central government.
Even if Maliki allies make up the biggest bloc in Iraq's next parliament, they will have to unite with one or two other coalitions to form a government, and Maliki may face challenges from coalition partners opposed to giving him a second term.
Final results may take several weeks. Ad Melkert, the U.N. special representative to Iraq, lauded the vote count on Wednesday as an "honest process" and urged candidates and parties to accept the results.
(Additional reporting by Aseel Kami and Waleed Ibrahim, writing by Jim Loney; editing by Mark Trevelyan)