Raja noted that Doval's statements were not in line with the stance maintained by the Central government that the move to revoke Article 370 is India's internal matter.
The NSA also said Pakistan co-opted small Kashmiri separatist groups and fomented unrest by arousing fear and suspicion about India, which later took on a religious colour.
Ajit Doval told a select group of journalists that there are Pakistani communications towers along a 20-km stretch of the border from where they are sending messages to terrorists.
Doval also said that the police and central armed forces are present to handle law and order in the state and to prevent Pakistan from creating more mischief through proxies and terrorists.
Doval's visit was on the invitation of his Russian counterpart Nikolai Patrushev.
Doval, who had recently spent around 11 days in the Valley amid the security lockdown, returned to Delhi recently. It was Doval's first direct briefing for the Home Minister at his office.
The NSA also ensured smooth coordination between all arms of security forces in J-K and gelling them with available intelligence inputs for smooth operations in the hinterland.
However, Eid prayers were disallowed at the Syed Yaqoob Shah shrine at Sonawar in Srinagar and the famous Hazratbal shrine.
NSA Ajit Doval, who has been visiting different parts of the Valley, including the troubled hot-spots of Anantnag, Sopore and Shopian, for the past week.
The NSA, who has been spending time visiting areas that were known as hotbeds of separatists, enquired from the animal traders about the weight and price of the sheep being sold for Eid ul Adha.
The NSA, accompanied by his aides and senior police officers, visited the Eidgah locality and stopped at various places to interact with locals.
The decision was taken as a precautionary measure to maintain law and order, a day after restrictions in some parts of the civil lines areas of the city and Dal Lake were eased to allow free movement.
BJP on Thursday hit back at Congress leader Ghulam Nabi Azad for alleging that National Security Advisor Ajit Doval's visit to Jammu and Kashmir was orchestrated with money.
Azad was reacting picture of NSA Ajit Doval interacting with locals in Jammu and Kashmir's Shopian.
Doval was seen interacting with a few people in a shut-down market over food and inquired about their well being. He also explained to them about the Centre's decisions.