Condemning the attacks, the Prime Minister also told the members that they should give their views to the committee constituted to address the issue.
"I share your concerns. Indians have a right to live with dignity anywhere in India," the prime minister told the members of the Northeast Forum of Parliament.
"Its deplorable and condemnable. Home minister has set up a committee to go into these causes in a systematic manner and prevent them," he said.
Some northeast parliamentarians joined the protesting group of students.
Manmohan Singh also told the forum members to "work closely" with the committee on northeast affairs.
The union home ministry has formed a six-member panel to suggest remedial measures to end discrimination against the northeast people.
The meeting came in the wake of attacks against northeast students, including the killing of Arunachal Pradesh student Nido Tania.
Speaking to IANS, Sikkim MP P.D. Rai said the delegation met the prime minister at the parliament house.
The other delegation members included Tripura MPs Khagen Das and Baju Banriyan, Mizoram MP C.L. Ruala and Meghalaya MP Vincent H. Pala.
Some northeast parliamentarians later joined the protesting group of students and activists demanding justice for Tania, son of Arunachal Pradesh legislator Nido Pavitra, at the city centre.