Obama blamed himself for not being forceful enough in challenging some of the misconceptions about him, including the false belief held by some Americans that he is a Muslim.
"I do think that, you know, in attempting to satirise something, they probably fuelled some misconceptions about me instead," he said.
"But, you know, that was their editorial judgment. And as I said, ultimately, it's a cartoon, it's not what the American people are spending a lot of their time thinking about."
The cover of The New Yorker magazine, which went on sale on Monday, depicts Obama in what many see as "Muslim clothing" - sandals, robe and turban - while Michelle Obama, his wife, has an assault rifle slung over one shoulder and is dressed in camouflage and combat boots.
Bill Burton, Obama's spokesman, termed it "tasteless and offensive".
David Remnick, The New Yorker editor, has defended the cover, saying it was satirical and was chosen because it had something to say.