Thamer al-Sabhan is the first Baghdad-based Saudi ambassador in a quarter century, but while full diplomatic relations are restored, there is still significant hostility to Riyadh in some quarters and there have already been calls for the envoy's expulsion.
The foreign ministry summoned Sabhan "to inform him of its official protest regarding his media statements that represented interference in Iraqi internal affairs," it said in a statement.
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Iraq turned to Shiite militia forces in 2014 to help counter an IS onslaught that overran large areas north and west of Baghdad, and they have played a key role in the fight against the jihadists.
But militias and their affiliates have also carried out abuses including summary executions, kidnappings and destruction of property, and many members of the Sunni Arab and Kurdish minorities view them with suspicion.
The foreign ministry defended the Hashed al-Shaabi, "which is fighting terrorism and defending the sovereignty of the country, and works under the umbrella of the state."
Shiite politicians had earlier reacted angrily to the Saudi ambassador's comments, but the country's largest Sunni bloc defended him.
"The remarks of the Saudi ambassador indicate clear hostility and blatant interference in Iraqi affairs," Khalaf Abdulsamad, the head of the Dawa parliamentary list, said in a statement.
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