The four-member delegation was led by Manipur MP Thokchom Meinya.
A member of the delegation, Malem Ningthouja, said after the meeting that the prime minister promised to recommend to the home ministry to expedite investigations into the death of both Loitam Richard and Dana Silva M Sangma.
The prime minister was also quoted as assuring maximum efforts to deliver justice in the two cases and measures to prevent such incidents from recurring.
The delegation expressed concern to the prime minister over targeted violence and discrimination on the students, migrant workers, job seekers, and tourists from the northeastern states in other parts of India.
"The prime minister also informed that there had been several instances of crimes against humanity and that the government had been taking up measures to control it. However, he denied racism in India and institutionalised discrimination against the people hailing from the northeast," Ningthouja said in a statement.
The delegation comprised representatives of Justice for Richard, and Manipur Students Association. The delegation gave a petition, which had gathered 26,250 signatures during a online campaign, to the prime minister.
Loitam, 19, was found dead under mysterious circumstances on April 18 in his hostel room at the Acharya NRV School of Architecture in Madanayakanahalli, some 30 km from Bangalore. He was lying dead cold in his room the next day with several marks of obvious assault on the face and head.
Sangma, a 21-year-old Amity University student and nephew of Meghalaya Chief Minister Mukul Sangma, committed suicide April 23 in Gurgaon after being allegedly insulted by an exam invigilator.