Indian Kashmir largely shut down amid heavy security on Friday after troops shot dead four people during a protest over a paramilitary raid on an Islamic school.

Shops, banks, schools and most government offices were closed in towns across the region, after a separatist leader called a three-day strike to protest Thursday's killings.

Srinagar, the main city in the region, was largely deserted after hundreds of police and paramilitary troops were deployed on the streets to halt any demonstrations over the deaths, an AFP reporter on the scene said.

Although authorities have not officially declared a curfew in the troubled Himalayan region, residents said they were not being allowed to go about their business.

"Early in the morning, troops appeared all around my neighbourhood disallowing people from coming out onto the streets," a resident of the old part of Srinagar, Farhan Ahmed, said by phone.

"It is undeclared curfew," he said.

Troops fired on protesters on Thursday, after residents of the district of Gool gathered to demonstrate against what they said was a desecration of the Koran by troops during their search of a madrassa.

They gathered outside a base of the Border Security Forces (BSF) in Gool region, 230 kilometres (143 miles) south of Srinagar.

Residents accused BSF troopers of beating up a caretaker and desecrating a Koran, during a search for militants inside the madrassa in Gool late on Wednesday.

Police officers initially said six protesters were killed in the firing. But inspector-general of police, Rajesh Kumar, clarified on Friday that only four had died.

"The fact is that the number of dead is four. The confusion was because we were busy in dealing with law and order and also due to the spotty nature of telecommunications in the mountainous area," Kumar told AFP.

He said 37 protesters were also injured in the incident.

The region's chief minister, Omar Abdullah, condemned the shootings while India's Home Minister Sushil Kumar Shinde ordered an investigation, saying the deaths were regrettable.

A top separatist leader, Syed Ali Geelani, called for a shutdown to protest the killings.

Most separatist leaders have been detained or put under house arrest to prevent them from leading protest rallies, sources said.

Chairman of the pro-independence Jammu Kashmir Liberation Front (JKLF) called for a protest before he was detained by police on Thursday.

The main university in the region postponed examinations scheduled for Friday without announcing any fresh dates.

Elsewhere, in Pakistani Kashmir's main city Muzaffarabad around 500 protesters took to the streets, chanting slogans and burning the Indian flag, to condemn the forces' actions.

A revolt against Indian rule has going on for decades in Kashmir, the country's only Muslim-majority state.

The insurgency has been a regular source of tensions between residents and security forces, which often spill over into violence.

About a dozen rebel groups have been fighting Indian forces in Kashmir since 1989, either for independence or for a merger with Pakistan. The fighting has left tens of thousands, mostly civilians, dead.

Nuclear-armed rivals India and Pakistan have each administered part of Kashmir since the partition of the subcontinent after the end of British rule in 1947.

Each country claims the territory in full.