In his first comments on the Iranian leader's statement that the 2001 terrorist attacks on America may have been orchestrated to bolster the US economy and ''save the Zionist regime'', Mr Obama told BBC Persian that ''for him to make a statement like that was inexcusable''.
US and European diplomats walked out of the UN General Assembly hall on Friday when Mr Ahmadinejad delivered his remarks about the September 11 attacks on New York and the Pentagon.
Envoys representing Australia, Canada, Costa Rica and New Zealand also left during the speech.
The interview with BBC Persian is part of Mr Obama's attempt to communicate directly with the Iranian people as the US and other nations increase pressure on Mr Ahmadinejad's government to comply with UN demands that it halt uranium enrichment.
''To have a President who makes outrageous, offensive statements like this does not serve the interests of the Iranian people, does not strengthen Iran's stature in the world community,'' Mr Obama said.
The US, Britain, China, France, Germany and Russia were united last week in telling Mr Ahmadinejad to comply with UN Security Council demands or remain under trade and financial sanctions. The council wants Iran to cease uranium enrichment and answer the International Atomic Energy Agency's questions about whether the effort is designed to achieve a weapons capability.
In his speech to the General Assembly on Friday, Mr Obama said while he was willing to negotiate, ''the Iranian government must demonstrate a clear and credible commitment, and confirm to the world the peaceful intent of its nuclear program''.
Mr Obama told BBC Persian that Mr Ahmadinejad's address ''defies not just common sense but basic sense - basic senses of decency that aren't unique to any particular country - they're common to the entire world''.
He drew a distinction between the Iranian people and their government, saying that when the September 11 attacks took place there was ''a natural sense of shared humanity and sympathy expressed within Iran''.
''It just shows once again sort of the difference between how the Iranian leadership and this regime operates and how I think the vast majority of the Iranian people who are respectful and thoughtful think about these issues,'' he said.