The matter is a delicate one in Poland, which suffered a brutal Nazi occupation during World War 2 and has long campaigned against suggestions it bore any responsibility for the slaughter of some 6 million European Jews.
"The White House will apologise for the outrageous mistake," Foreign Minister Radoslaw Sikorski wrote on his Twitter account. "It's a pity that ignorance and incompetence overshadowed such a momentous ceremony."
Sikorski said he did not suspect Obama of ill will and blamed the "grave mistake" on the White House's speech writers and press service.
US National Security Council spokesman Tommy Vietor said:
"The president misspoke - he was referring to Nazi death camps in Poland. We regret this misstatement, which should not detract from the clear intention to honour Mr. Karski and those brave citizens who stood on the side of human dignity in the face of tyranny."
Polish Prime Minister Donald Tusk, speaking after the issue filled Polish media on Wednesday, said: "When somebody says 'Polish death camps' it is as if there were no Nazis, no German responsibility, no Hitler."
He urged Washington to make up for the mistake by actively supporting Warsaw's drive against such rhetoric.
The posthumous award for Jan Karski was to honour him for bringing some of the first eyewitness testimony of the Holocaust to the outside world, after he was smuggled into the Warsaw Ghetto and a Nazi camp.
Karski travelled to London, Washington and elsewhere urging action to prevent the mass extermination of Jews.
Israel's Yad Vashem institute has awarded Karski the Righteous Among the Nations title for his efforts to aid Jews, and to more than 6,300 other Poles, more than any other nationality, despite the fact that Poland's history is littered with anti-Semitism.
Some 3.3 million Jews lived in Poland before 1939. Most perished during World War Two, among nearly 6 million Polish deaths in total.
A museum dedicated to the history of Polish Jews is now under construction in the capital Warsaw.
"We should use this huge gaffe to make sure nobody, nowhere in the world, ever says that again," said Lech Walesa, Poland's sole Nobel Peace Prize winner.
