Baghdad on Tuesday said Jordan's hosting of a meeting of Sunni Iraqis opposed to the Shiite-led government was "unacceptable".
On Friday Iraq recalled its envoy to Amman without giving a reason, but the move came days after a meeting of some 300 Sunni clerics, tribal leaders, insurgent commanders and businessmen in the Jordanian capital.
Delegates described a Sunni Islamist insurgency that has taken hold of swathes of Iraq in recent weeks as a "popular revolt".
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Islamic State jihadists are spearheading the campaign, which began in the Iraqi city of Mosul on June 9 and has since swept large parts of the country's northern and western provinces.
The Iraqi government described those attending the meeting as "enemies of the political system and social fabric of Iraq".
"The cabinet considers the hosting of these conferences an unacceptable hostility towards the Iraqi people by a friendly, sister country," the cabinet said, and asked that the foreign ministry follow up on the issue.
Iraq's Shiite Prime Minister Nuri al-Maliki has decried what he describes as foreign meddling in his country, and has accused countries in the region of arming and funding militants.
Iraq was almost torn apart in 2006-2007 when the bombing of a revered Shiite shrine in Samarra, north of Baghdad, triggered a wave of sectarian slaughter between Shiite militias and Al-Qaeda-allied Sunni militants.