During the meeting that lasted 15 minutes, Kejriwal voiced concern over the prevailing atmosphere at the institution arising out of an event to protest against the hanging of Parliament attack convict Afzal Guru.
The President of JNU Students' Union, Kanhaiya Kumar, was arrested following that event.
Sources said the Chief Minister told Singh that the issue got complicated due to police action against the students.
The Chief Minister also discussed with the Home Minister a few administrative issues relating to the Delhi government, they said.