The foreign ministry said Mr Comey had suggested in a Washington Post article that some Poles were accomplices.
After the summons US envoy Stephen Mull said he made it clear the US believed "Nazi Germany alone" was responsible.
Six million Polish citizens were killed by the Nazis during World War Two, half of them Jewish.
In the Washington Post article on Thursday, aimed at raising education about the Holocaust, Mr Comey wrote: "In their minds, the murderers and accomplices of Germany, and Poland, and Hungary, and so many, many other places didn't do something evil.
"They convinced themselves it was the right thing to do, the thing they had to do."
The words sparked a storm of protest in Poland.
President Bronislaw Komorowski told Polish television the comments were an "insult to thousands of Poles who helped Jews".
Prime Minister Ewa Kopacz said: "To those who are incapable of presenting the historic truth in an honest way, I want to say that Poland was not a perpetrator but a victim of World War Two. I would expect full historical knowledge from officials who speak on the matter."
Ambassador Mull, who on Sunday attended ceremonies marking the 72nd anniversary of the Warsaw Ghetto uprising against the Nazis, said that any suggestion that "Poland, or any other countries other than Nazi Germany, bear responsibility for the Holocaust, is a mistake, harmful and insulting".
After Sunday's summons he added:  "I made clear that the opinion that Poland is in any way responsible for the Holocaust is not the position of the United States.
"Nazi Germany alone bears responsibility. I now have a lot of work before me to make things right in this situation."
But Mr Mull also said he believed the wider message of the article was that many people had either aided the Nazis or not done enough in response to the atrocities, including in the US.
The Washington Post on Sunday published a column criticising Mr Comey's comments.
The Nazis ran death camps in Poland during the brutal 1939-45 occupation.
Correction 20 April 2015: In an earlier version of this report, comments made by the Polish ambassador to Washington were incorrectly attributed to Stephen Mull.
Poland has summoned the US ambassador and demanded an apology over comments on the Holocaust by FBI director James Comey.