Although he shuns overt political engagement, al-Sistani's word holds sway in Iraqi politics and leaders frequently seek his advice.
Al-Maliki, designated by parliament to put together a unity government, met Condoleezza Rice, the US secretary of state and Donald Rumsfeld, the secretary of defence, in Baghdad a day earlier.
The incoming prime minister won al-Sistani's endorsement on Thursday for his plan to disband militias, which the United States believes is the key to calming sectarian strife.
The ayatollah told al-Maliki that security should be his priority.
A statement by al-Sistani's office said: "Weapons must be exclusively in the hands of government forces and these forces must be built on a proper national basis so that their loyalty is to the country alone not to political or other sides."
Al-Maliki plans to integrate militias, many of them linked to Shia political parties, into the army and police. To ensure their loyalty to the central government, he wants to appoint defence and interior ministers without links to militias.
Former militiamen who have joined government forces, especially those run by the Shia-led interior ministry, have been widely accused by Sunni Arabs of operating as death squads targeting Sunni civilians.
Attempts by previous Iraqi governments to abolish militias have failed, and their numbers have grown, in part because US and Iraqi forces have been unable to guarantee public safety.
Al-Maliki in the holy city of Najaf
The leader of one major militia, Muqtada al-Sadr, refrained on Thursday from endorsing calls to disband his Jaish al-Mahdi (al-Mahdi Army). After a separate meeting with al-Maliki, he was asked if he would give up his militia.
He said: "All groups inside or outside the government work for the people's interest and service."
Al-Maliki has until late May to present his Cabinet to parliament, the final step in building a national unity government.
The US believes a government of Sunnis, Shia and Kurds will help calm sectarian passions and reduce the fighting against US-led forces so the 130,000 American troops can begin to leave the country.
Sectarian tensions rose after the February 22 bombing of a Shia shrine in Samarra, triggering reprisal attacks against Sunni mosques and religious leaders.
Lieutenant-General Peter Chiarelli, the second-ranking US general in Iraq, has said that militias pose an urgent threat to the country's stability.
In a briefing on Thursday, Major-General Rick Lynch, a US spokesman, said: "We are not seeing widespread militia operations across Iraq."
He said ethno-sectarian attacks had dropped by half in Baghdad over the past week. Lynch said US forces had found no "widespread movement" of Shia and Sunnis away from religiously mixed areas, despite reports to the contrary by Iraqi officials.
"So we do not see us moving toward a civil war in Iraq," Lynch said. "In fact we see us moving away from it."