Pecker is a key witness in the case against the former US president, who is accused of falsifying business records to cover up hush-money payment
The early Wednesday strike led Iraq to say it would summon the Iranian ambassador.
In a letter to the United Nations Security Council and UN Secretary General Antonio Guterres, Iran's ambassador to the UN, Majid Takht Ravanchi, said his country has full respect for "the independence, sovereignty, unity and territorial integrity of the Republic of Iraq."
There were no American or Iraqi military casualties in the strikes.
"The operation was precise and targeted military objectives thus leaving no collateral damage to civilians and civilian assets in the area," the diplomat said in a letter released by the Iranian mission.
Iran "recalls its dedication to the maintenance of international peace and security and stresses that it does not seek escalation or war," he said.
Iraq's foreign ministry said Wednesday it would call in the Iranian ambassador because of the missile attack, which it called a violation of Iraqi sovereignty.
Iraq had already summoned the US ambassador after the US drone strike last Friday that killed top Iranian general Qasem Soleimani near Baghdad airport.
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