Candidates supporting the current prime minister have made strong gains in the south of the country according to Iraqi media.
The southern port of Basra and the Shiite holy city of Najaf are among key areas believed to have posted gains for al-Maliki allies. Iraqi secular parties are also thought to have gained votes because of disillusionment with religious parties.
Overall turnout in Saturday's provincial elections was 51 per cent, less than expected and less than previous polls, but the election passed without major violence.
The low turnout was blamed on confusion over the vote registration. Many Iraqis complained they had turned up at polling stations only to find their names was not registered to vote.
Road closures and vehicle bans designed to prevent car bombings are also thought to have deterred voters.
But those who did cast their votes praised a government-led purge of Shia militias in Basra and southern regions last year.
"Al-Maliki ended the militiamen's reign of terror," said Faisal Hamadi, 58, after voting in Basra. "For this he deserves our vote."
Victory for al-Maliki's allies would come at the expense of the Supreme Islamic Iraqi Council, the biggest Shiite party. It would also strengthen his position ahead of national elections later this year.
Sunni voters boycotted the 2005 provincial elections in fear of reprisals and in protest at the US invasion of their country.
However on Saturday Salaheddin, Saddam Hussein's home province, recorded the largest turnout at 65 per cent. Anbar, the former Sunni rebel stronghold which had a turnout of less than one per cent four years ago, recorded 40 per cent turnout the Iraqi election commission said.
Sunni leaders are also hoping to capitalise on their role in dramatically curbing insurgency violence.
Tribal leaders who formed Awakening Councils, abandoning the insurgency to fight al Qaeda, are now hoping for seats on provincial councils.
Voting took place in 14 of Iraq's 18 provinces and official results are not expected for several days.
US President Barack Obama congratulated the people of Iraq on the smooth-running elections.
"This important step forward should continue the process of Iraqis taking responsibility for their future," he said in a statement.
More than 14,400 candidates stood for 440 seats in councils, which appoint the provincial governor and oversee finance and reconstruction, with a combined budget of $2.5 billion (£1.8 billion).
The elections took place under tight security with many streets closed to traffic to prevent car bombings.
Violence in Iraq has fallen to its lowest levels since the 2003 US-led election new figures have shown.
A total of 191 Iraqis were killed in violence last month (JAN), including 27 soldiers and 24 policemen. Just over 400 Iraqis were wounded.
"I consider the toll is due to the efforts of the Iraqi security forces, and the support of the Iraqi people, which helped to keep down the terror," said defence ministry spokesman Major General Mohammad al-Askari.
Gordon Brown praised Iraqis for "braving the threat of intimidation"
to take part in the elections.
"That so many Iraqis once again braved the threat of intimidation to vote in provincial elections sends the clearest possible signal of their commitment to Iraq's sovereign, democratic future," he said.Click here for the Telegraph