The Iraqi government launched a probe into the most recent incident earlier this week that injured one person when five rockets were fired at the US outpost. Two rockets hit a canteen area.
Mr Abdul Mahdi issued a statement after the attack denouncing the move. He also ordered an investigation and security forces to prevent further repeat incidents.
“We denounce the continuation of these outlawed actions that have the goal of weakening the Iraqi state and violating its sovereignty and the sanctity of diplomatic missions on its soil,” he said.
The US has blamed Iran-backed militias for repeated rocket attacks on the US embassy and Iraqi military bases housing American troops, a near-weekly occurrence in recent months.
Tensions have soared since the January 3 US airstrike that killed Iran’s Revolutionary Guard Quds force head Qassim Sulimani and Iraqi militia leader Abu Mahdi Al Muhandis.
A mass protest attacked the US embassy in the wake of the killing, setting fire to the entrance area and leading to staff being evacuated from the outpost. The US deployed additional troops to secure the site and Iraqi counter-terror units deployed to clear the streets around the compound.
The government is also contending with nearly four months of mass protests, their response to which has left over 600 dead and tens of thousands wounded.
In the overnight call, Mr Abdul Mahdi also stressed the importance for everyone to respect Iraq's sovereignty. In the wake of the Sulimani strike, the Iraqi parliament voted in a non-binding resolution to end a deal for US troops to be based in the country to assist in counter-ISIS operations.
It is unclear if the government will enforce the resolution or if the US will comply.
State Department spokeswoman Morgan Ortagus said that Mr Pompeo raised the issue of the Iran-backed militias as well as sovereignty in the call with Mr Adel Mehdi.
"The Secretary underlined once again that these attacks demonstrate a wanton disregard for Iraqi sovereignty and a failure to rein in these dangerous armed groups," she said.