In his phone call Mohammed Shia al-Sudani, Rubio "highlighted the urgency in disarming Iran-backed militias that undermine Iraq’s sovereignty, threaten the lives and businesses of Americans and Iraqis, and pilfer Iraqi resources for Iran," according to a state department press release.
"The Secretary reiterated the US commitment to working closely with Iraqi partners to advance our shared interests: safeguarding Iraqi sovereignty, bolstering regional stability, and strengthening our economic ties," the state department added.
American officials have issued several private warnings to the Iraqi government since January over the Tehran-backed armed militants, telling Baghdad it could target the groups with airstrikes unless it acted to disband the militias operating on its soil.
The militia commanders, from groups including Kata'ib Hezbollah and Nujaba, were quoted by Reuters in April as saying their main ally, Iran's Revolutionary Guards (IRGC), had given them its blessing to avoid a conflict with the US and Israel.
"Trump is ready to take the war with us to worse levels, we know that, and we want to avoid such a bad scenario," Reuters reported at the time citing a commander of Kata'ib Hezbollah, the most powerful Shi'ite militia.
However, Iraqi politician Muthal al-Alusi denied the report, calling the claims a nominal effort to protect involved politicians. He told Iran International on April 7 that "in practice, the real militias have received advanced weapons, and their participation on the battlefield may be completely evident."
The militias form part of the Islamic Resistance in Iraq, an umbrella group claiming responsibility for numerous attacks on Israel and US forces during the Gaza war.
The developments come as Iraq seeks to strike a balance in its relations with neighbor Iran and superpower the United States, with the militias having grown significantly since the 2003 US invasion.
Washington had warned Baghdad against revenge attacks by these groups after recent strikes on the Iran-backed Houthi movement in Yemen.