In an interview published on Monday in the American daily USA Today, Maliki said he had formed a committee to oversee a political and military strategy to isolate and confront the militias, but that this would take time.
"The initial date we've set for disbanding the militias is the end of this year or the beginning of next year," he told the newspaper.
"The problem that we face in disbanding militias -- and the militias have to be disbanded -- is that there are procedures, steps that need to taken, which take time," he explained, in an interview conducted in his Baghdad palace.
Maliki was speaking at a time of mounting frustration among US officials in Washington and Baghdad, who have urged his government to take quicker and more decisive steps to get the guns off Iraq's streets.
In particular, coalition commanders want permission to launch a large-scale operation to clear Sadr City, a sprawling east Baghdad slum that is home to 2.5 million Shias and several thousand Mahdi Army militiamen.
In his interview, however, Maliki said that -- while he would allow precision raids against precise targets -- he had vetoed any bigger push to avoid hurting and alienating the area's large civilian population.
"We have told the Americans that we don't mind targeting a Mahdi Army cell inside Sadr City," he said. "But the way the multinational forces are thinking of confronting this issue will destroy an entire neighbourhood.
"Of course it was rejected," he said.
Maliki was also critical of heavy-handed American counterinsurgency tactics in Iraq in the three-and-a-half years since US-led forces overthrew Saddam Hussein, blaming the coalition for the poor performance of Iraqi forces.
"The problem we are facing is the way the army, police and security forces were formed by the multinational forces, during (former Coalition Provisional Authority chief administrator Paul) Bremer's time," he said.
"These forces were built randomly, and that led them to be weak and infiltrated by militias," he charged, according to a transcript of his interview on USA Today's website.
Sent by Washington to run Iraq in the aftermath of the US-led invasion, Bremer disbanded the entire Saddam-era military and started building new security forces from scratch amid mounting insurgent violence.
Today, Iraq's army and especially police are often accused of collaborating with sectarian militias. US generals admit privately that in their haste to build a local force they incorporated entire militia units into the police.
"The phenomenon of co-operating with militias exists in the interior ministry and, to a lesser degree, the defence ministry," Maliki confirmed.
"It is not a matter of investigation. This is something that is not hidden, people know about it," he said. "We are still paying the price for the mistakes made by the Multinational Forces in establishing the interior and defence ministries in a random way and according to wrong theories."
Maliki decried current US military strategy in fighting militias and militant groups like al Qaeda as the "wrong approach."
"Terrorism and militias -- especially militias -- cannot be dealt with only by using tanks, guns and aircraft. You need security cells that gather information and infiltrate the areas where they operate," he said.

Copyright AFP (Agence France-Presse), 2006