He cautioned that the casualties of both civilians and security personnel in the violence-hit state should be minimum.
The minister was, in turn, briefed by top officials on the prevailing situation in Kashmir and the infiltration bid along the Line of Control (LoC) in Uri sector in Kashmir.
National Security Adviser Ajit Doval, Home Secretary Rajiv Mehrishi and chiefs of intelligence agencies and other top civil and security officials attended the meeting, sources said here.
The meeting was held even as reports from Srinagar said five civilian protestors were killed in firing by security forces in fresh violence in the Kashmir Valley on Tuesday, taking the to;; to 65 since the July 8 killing of a popular rebel commander.
Pramod Kumar, commandant of the 49 Battalion of the Central Reserve Police Force (CRPF), was killed on Monday after four militants hurled a grenade and opened fire at a security patrol in an old city area of Srinagar.
There have been reports of violence and stone-pelting in Budgam and Anantnag districts as well, sources said.
At the meeting, Rajnath Singh also reviewed the overall security scenario in Assam, which also saw militant attacks.
Suspected militants exploded five bombs in Charaido and Tinsukia districts as the north-eastern state was celebrating the 70th Independence Day on Monday.
On August 5, 14 persons were killed and at least 20 injured by National Democratic Front of Bodoland (Songbijit) militants in Kokrajhar district of Assam.