As precautionary measure authorities have suspended mobile Internet services in Kulgam district.
A purported video of Raqib Ahmad, shot before he was killed, went viral on social media on Saturday.
On Sunday, a deputy superintendent of police, an army jawan and the three Jaish-e-Mohammad (JeM) militants were killed during the encounter in the district's Turigam area.
Thakur, who is in his late 30s, first got a job in the social welfare department and was later appointed as a lecturer at a government college in view of him having a master's degree in Zoology.
The cops said five militants were killed in the encounter and weapons and warlike stores were recovered from the spot.
A Police Spokesman said that despite warning, the civilians had gathered near the encounter site, where an explosion took place, resulting in civilian casualties.
Political parties in Jammu and Kashmir express anguish over civilian deaths near Kulgam encounter site
Immediately after the gunfight ended and the forces withdrew from the spot, civilians rushed to the encounter site where an explosive substance went off resulting in the death of six civilians.
Security forces launched a cordon and search operation in Laroo area of Kulgam district in south Kashmir following specific information about the presence of militants in the area.