Pompeo is now on a Mideast tour, bringing the Trump administration's anti-Iran message to the region.
In a statement, the ministry said it lodged an official protest with Warsaw for hosting the event.
The move came shortly after the Iranian Foreign Ministry on Sunday summoned the Polish Charges D'Affairs, Wojciech Unolt, to protest an Iran-focused conference in Warsaw next month. The US president has since ordered a review of the costs of American troops being stationed in Germany, a sign that he may pivot to eastern Europe. Among the Mideast leaders invited was Israeli Prime Minister Benjamin Netanyahu, whose attendance might complicate participation by some Arab countries.
The Polish foreign ministry could not be reached for comment, Reuters news agency said.
The statement quoted an unnamed Iranian official as saying that if the summit goes ahead, Iran will resort to unspecified "counter-action" toward Poland, without elaborating.
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Relations between Tehran and Washington are highly fraught following the decision in May by President Donald Trump to pull the USA out of a 2015 nuclear deal between Iran and six major powers and to reimpose sanctions.
While Poland has supported the EU's attempts to hold onto the landmark nuclear deal after US President Donald Trump pulled Washington out of the agreement, Warsaw has expressed the belief that the deal alone would not stop Iran from "destabilizing" the region.
"Reminder to host/participants of anti-Iran conference: those who attended last United States anti-Iran show are dead, disgraced or marginalized".
A State Department spokesman acknowledged that Poland, like other European nations, supports the global accord from which Mr Trump exited a year ago on ending the Iranian nuclear program.
Iranian Foreign Minister Mohammad Javad Zarif criticised Poland on Friday for hosting the meeting and wrote on Twitter: "Polish government can't wash the shame: while Iran saved Poles in World War II, it now hosts desperate anti-Iran circus".
Pompeo is expected to call for increasing pressure on Iran and push for unity among Gulf neighbors still embroiled in a bitter dispute with Qatar.