"She has expressed her personal apologies and the apologies of the government of the United States. She confirmed that the United States will take immediate actions to prevent such actions from happening again," al-Maliki's office said.
Tom Casey, the deputy state department spokesman, said: "She told the prime minister that we were investigating this incident and wanted to gain a full understanding of what happened."
Rice and al-Maliki "agreed on the importance of working closely together in the time ahead on a transparent investigation," Casey added.
Yassin Majid, an adviser to the prime minister, said the two also agreed to hold any wrongdoers accountable.
Al-Maliki had condemned Sunday's shooting and vowed to punish the perpetrators and their employers.
"We will work to punish and halt the work of the security company which conducted this criminal act," state television quoted him as saying.
The 15-minute call came after Iraq's interior ministry said it had revoked Blackwater's licence.
The firm is responsible for US embassy security and the expulsion may severely curtail US operations in Iraq by stripping diplomats and other officials of protection.
The two other private security firms employed by the US state department to protect its personnel in Iraq are Dyncorp and Triple Canopy.
Blackwater said it had not been formally notified of any expulsion. The US state department also said Washington had not been informed of the licence cancellation.
Conflicting accounts were reported of the incident in which, according to the US embassy in Baghdad, a diplomatic convoy was attacked, and security guards opened fire in response.
Estimated 30,000 private security "contractors" in Iraq often referred to as shadow armies and mercenaries
US figures say in the first gulf war, ratio of private contractors to troops one to 60, now about one to three
Little known about who security firms are accountable to
Accused of being overly aggressive and above the law
Blackwater has secured more than $500m in federal contracts since 2000 - two thirds of those contracts known as "no bids"
Landed first big contract in Iraq in 2003, protecting Paul Bremer, the-then US top administrator in Iraq, for 11 months for $21m
Employs 1,500 security personnel in Iraq, specialising in transporting so-called high-value targets
US military destroyed Falluja in 2004, weeks after four Blackwater employees were killed there
Has also stirred up controversy in Potrero, a small US town along the California-Mexico border where it wants to build a huge training camp
Iraq's interior ministry said eight civilians were killed and 13 wounded when Blackwater contractors opened fire on civilians in the predominantly Sunni neighbourhood of Mansour in western Baghdad after mortar rounds landed near their convoy.
General Abdul Kareem Khaleh, an interior ministry spokesman, said Blackwater guards "opened fire randomly at citizens".
"We have withdrawn its licence" and will "deliver those who committed this act to the court", he added.
Anne Tyrrell, a company spokeswoman, said late on Monday: "Blackwater's independent contractors acted lawfully and appropriately in response to a hostile attack in Baghdad on Sunday."
The state department could not say which Iraqi laws Blackwater or its employees might be subject to, the chain of command its employees answer to.
The US embassy said it was seeking clarification on the legal status of security contractors and whether Blackwater employees could be prosecuted in Iraq.
Khaleh said the security guards "do not have immunity, as immunity is granted only to the multi-national forces … [They] are subject to the obligations of the Iraqi penal law".
The moves by the Bush administration appear unlikely to forestall a congressional inquiry into not just Sunday's events but the government's increasing reliance on the use of contractors in Iraq.
"The controversy over Blackwater is an unfortunate demonstration of the perils of excessive reliance on private security contractors," Henry Waxman, the Democratic chairman of the House Oversight and Government Reform Committee, said.
He said his committee would hold hearings to determine "what has happened and the extent of the damage to US security interests".