The Ministry sought a report from the Maharashtra government because Pune police may have "exceeded" their brief by deporting Neetu Singh, a fourth year student of editing at FTII on December 5.
Pune DCP (Special Branch) Ravindra Sengaonkar had said the decision to deport her was taken after she was found involved in "anti-national activities".
The DCP refused to divulge further details of the case which has been taken up by All India Democratic Women''s Association (AIDWA), alleging that Neetu''s deportation was ordered by Pune Police at the instance of her husband Amaresh Singh.
Singh is influential person and a nominated Member of Parliament in Nepal.
Neetu was in touch with the organisation since June 2008 with complaint of harassment against her husband who wanted her to quit the course, AIDWA''s Kiran Moghe had said.
"If she has indulged in anti-national activities here, police should have filed a case and tried her in India instead of sending her back to Nepal", Moghe had said while alleging that the police had acted in connivance with Amresh Singh.