Two Muslims, Ajaz Ahmad and Javad Khan, were shot dead in the southern districts of Anantnag and Pulwama overnight, police said.
Khan was a government employee, but the motive behind the killings was not immediately known. No group claimed responsibility for the deaths.
Indian troops shot dead an insurgent in the forests of northern Kupwara district late on Saturday, police said.
Meanwhile, authorities set free Salim Zargar who was arrested on 18 April 1990, in the summer capital Srinagar shortly after the start of the insurgency.
Zargar was associated with the Students Liberation Front, which ceased to exist in 1993.
The front was a junior wing of the Jammu Kashmir Liberation Front (JKLF), whose chairman Yasin Malik received Zargar Sunday.
Friends and family welcome Salim
Zargar following his release
The JKLF, which wants divided Kashmir to be independent of both India and Pakistan, gave up fighting Indian troops in 1994 and said it would press the separatist cause politically.
More than 40,000 people have died in the resistance since 1989.
Separatists put the toll between 80,000 and 100,000.
At least 167 people have died in the fighting since India and Pakistan entered a 26 November ceasefire on the Kashmir borders.
Both India and separatists say the frontier truce does not apply to their operations inside the province.