"The fact that a foreign element wants to interfere in the affairs of Iraq and dominate the country progressively is the main problem for the development and well-being of the Iraqis."
Washington and Baghdad are in negotiations aimed at signing a deal by the end of July to cover the presence of foreign troops beyond 2008 when the current UN mandate expires.
Iraqi media reports have said the US is seeking to keep as many as 50 bases indefinitely, suggestions that have upset Tehran.
US officials have denied having any such plans.
Before leaving Tehran, al-Maliki thanked Iran for its "ceaseless" support of Iraq, state television said.
"Definitely this was a fruitful trip," he said.
"This trip was definitely a step forwards in the aims set by both nations, I hope that they are materialised."
The two sides also signed a memorandum of understanding on defence, relating to border issues and mine and body clearance from their 1980-1988 war, Parviz Davoudi, Iran's first vice-president, said.
Meanwhile, on the ground, violence continued unabated in Iraq.
A roadside bomb killed at least four people, including one Iraqi soldier, and wounded at least 12 other people, when it exploded near an Iraqi army patrol in Karrada district, central Baghdad, police said.
US forces killed five members of al-Qaeda in Iraq and detained 13 others in operations on Sunday and Monday, the US military said.
In one operation in northwest Iraq, the soldiers came under heavy fire and called in air support, the US military said.
In a separate incident, armed men stormed a house and killed two people in western Mosul, 390km north of Baghdad, Iraqi police said.
And in the city's western part, fighters killed one policeman while he was on a foot patrol, police said.