During the 20 minute meeting, both leaders also discussed a series of developments in the state related to Article 35A that gives special status to Jammu and Kashmir, sources said.
The article empowers the state legislature to define permanent residents of the state and their privileges.
The meeting with the Home Minister comes amid reports that Jammu and Kashmir Governor N.N. Vohra, 81, is likely to resign.
She is also reported to have met Finance Minister Arun Jaitley.
Mufti had visited New Delhi earlier this month when she had met with Singh and also Prime Minister Narendra Modi.