Harvard's Faculty of Arts and Sciences had voted earlier this week to remove two economics courses that Swamy taught at the university's annual Summer School programme citing a controversial op-ed on Islamic terrorism in India that he had written for an Indian publication.
Faculty members felt Swamy's views in the piece were "reprehensible" and amounted to "incitement of violence".
The courses were dropped from next year's session after the faculty voted with an "overwhelming majority".
Reacting to the news, Swamy said in New Delhi that he had assumed Harvard would have sent its petition to him asking for his comments before taking any decision.
In response to Swamy's comments, the Faculty of Arts and Sciences said in an emailed statement to PTI that "members of Harvard's Faculty of Arts and Sciences each year vote to approve or amend the course list for Harvard Summer School".
It added that the Faculty had voted to approve the curriculum for the Summer School for the coming summer session with the exception of the two courses, "about which there was considerable discussion".
The Harvard Summer School is an annual programme that runs typically from June through August.
Swamy, who received a PhD in economics from Harvard in 1965 and had served as an assistant and associate professor, taught 'Quantitative Methods in Economics and Business' and 'Economic Development in India and East Asia'.
His July op-ed piece, in which he had recommended demolishing hundreds of mosques and suggested that only Muslims in India who "acknowledge that their ancestors were Hindus" should be allowed to vote, had created controversy at Harvard with students demanding that the university should not affiliate itself with anyone who expressed hatred towards a minority group.
Dean of the Summer School Donald Pfister had said courses included in the catalogue are chosen by individual departments.
"I find (Swamy's) position reprehensible, but on the other hand, it is our duty to support departments and their offerings," he said.
Swamy had termed Harvard's decision as a "dangerous principle" saying the university should have first sought his comments on the issue which was a normal procedure but that had not been done.