It said such incidents are racially discriminatory and painful to the victims.
The ministry's communication comes a day after a woman from Manipur alleged that an unidentified man spat on her and called her "corona" in northwest Delhi's Vijay Nagar area.
In a letter to chief secretaries of all states and Union territories, the ministry said it had come to its notice that people from the Northeast have been facing harassment after the occurrence of the deadly COVID-19 in the country.
There have been cases where people, including athletes and sportspersons, from the Northeast have been harassed by linking them to COVID-19.
"This is racially discriminatory, inconvenient and painful to them. It is requested that all law enforcing agencies in your State/UT may be sensitised to take appropriate action in cases of harassment when these are reported," it said.