The meeting was attended by National Security Advisor Ajit Doval, Home Secretary Rajiv Gauba, Intelligence Bureau (IB) chief Arvind Kumar, Research and Analysis Wing (RAW) chief Samant Kumar Goel and senior Home Ministry officials.
Informed sources said the Minister discussed internal security as well as the situation in Jammu and Kashmir where the Amarnath Yatra has been curtailed after the government warned of terror threats.
All Amarnath pilgrims as well as tourists have been told to leave "as soon as possible".
Shah spoke about the preparation to deal with terror attacks and deployment of security establishment in the Kashmir Valley amid inputs that Pakistan-backed terrorists were planning to target the Amarnath Yatra - an annual month-long Hindu pilgrimage which started on June 28 and was to end on August 15, the sources said.
Shah is reportedly planning to visit Jammu and Kashmir. This too was discussed, said a source.
The Home Minister was apprised about the situation on the border where some Pakistani soldiers were killed by Indian forces when they tried to infiltrate into Jammu and Kashmir on the night of July 31-August 1.
The Minister's meeting and the abrupt axing of the Amarnath Yatra on Friday and the security build up has set off yet another round of speculation about the Modi government's next move in Jammu and Kashmir.
Residents say the Kashmir Valley is in panic mode since the curtailment of the Amarnath Yatra, with people buying up essential goods to prepare for the worst.
( With inputs from IANS )