The police officers were travelling to Amshipora village, 60 kilometres south of the main city of Srinagar, to probe a local land dispute when the ambush occurred.
The separatists, dressed in army fatigues, first released unharmed two civilians who were travelling in the vehicle along with the driver before firing on the officers, inspector general of police Javid Gillani told AFP.
Read: Separatists kill two in Indian Kashmir
"They (police officers) were going for an investigation when their vehicle was ambushed. All the three were killed. They were unarmed," Gillani said.
Police and the army have launched a hunt for the militants, whose attack came an hour after another police officer was shot and injured in a separate incident further north.
After boarding the bus travelling on a highway in Pattan, the suspected rebels noticed the officer, who was from a special counter-insurgency group of the state police force, was among those onboard.
The rebels tried to hijack the bus before abandoning the move and shooting the officer, a police officer said on condition of anonymity as he is not authorised to speak to media.
"The militants fled after shooting the police officer when the bus stopped in a traffic jam," the officer said.
Separatists have been fighting Indian forces since 1989 for independence or a merger of the Himalayan territory with Pakistan. The fighting has left tens of thousands dead, mostly civilians.
Kashmir has been divided between India and Pakistan since the two countries won independence from Britain in 1947.
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