Hagel had jokingly asked Robert A Gandhi, the Indian-American Professor "you are not a member of the Taliban, are you?", before he rose to ask a question to the Defence Secretary at the event.
"He (Hagel) expressed regret for any trouble this caused the professor," the Pentagon Press Secretary, George Little, said, adding that such a remark by the Defence Secretary "was a comment directed at no one in particular," and a lame attempt at humour.
"They had a very good discussion and (Hagel) wanted to leave no impression that this joke was directed at anyone in particular, including the professor," Little said.
In a statement released by the University, Gandhi said he was honoured to hear the speech of the Defence Secretary and get response from him on his question of cyber weapons.
"I was honoured to attend Secretary of Defence Hagel's speech on Wednesday. I was able to ask a question, and I thoroughly enjoyed hearing his answer. Before I rose to ask a question, there was apparently some confusion that did not involve me," Gandhi said.
This controversy is not the first one Hagel has courted by his remarks.
During an interview he had said that "the Jewish lobby intimidates a lot of people up here" on Capitol Hill. He later regretted this during a Senate confirmation hearing saying, "I regret referencing the Jewish lobby. I should have said pro-Israel".
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