The latest death occurred when a man was hit on his head by a tear gas shell fired by security forces and died in a hospital in the northern village of Drugmulla, police said.
He was part of hundreds of rock-throwing protesters who clashed with government forces for a second straight day Wednesday as authorities enforced a curfew in Srinagar, Handwara and neighboring villages.
The clashes occurred even as shops and schools were closed and streets deserted due to a security lockdown and a daylong strike call by separatist groups.
Mehbooba Mufti, who recently took over as the top elected official in the Indian portion of Kashmir, said the killings would have a "negative impact" on her government's peace efforts in the region.
Police said a 70-year-old woman, who was hit by gunfire and was among a dozen injured during massive clashes between residents and government forces on Tuesday, died in a hospital Wednesday. Two others also died from army gunfire.
The protest and clashes in the northern town of Handwara erupted Tuesday following an allegation by residents that an Indian army soldier tried to sexually assault a teenage schoolgirl.
Indian military, police and government officials, wary of the killings escalating the conflict in the volatile region, ordered investigations.
"The incident will be investigated and anybody found guilty will be severely dealt with," Indian army commander Lt. Gen. D.S. Hooda said in a statement.
Rights groups, however, say such probes rarely yield any concrete results and are often aimed at calming public anger.
Police Inspector-General Syed Javaid Mujtaba Gillani said the soldiers fired at protesters when they tried to torch their bunker.
Shortly after the woman's burial, clashes broke out as villagers defied the curfew and hurled rocks at government forces, who responded by firing tear gas.
"She was working in her orchard 4 kilometers (2 miles) away from the protest site. The soldiers came and shot her. It's a plain murder," said villager Ghulam Mohammed Shah.
Later Wednesday, hundreds joined the funeral of two young men and shouted "Go India, go back" and "We want freedom."
Meanwhile, the separatist groups challenging India's sovereignty over Kashmir called for a general strike on Thursday and anti-India protests on Friday.
Anti-India sentiment runs deep among the mostly Muslim population of Kashmir, and human rights groups have long accused the Indian military of using rape and sexual molestation to oppress the local population.
Kashmir has been split between Indian and Pakistani control since the British colonialists left in 1947, but is claimed in full by both countries.
Rebel groups have been fighting since 1989 for independence from India or the Indian portion's merger with Pakistan. More than 68,000 people, most of them civilians, have been killed in the armed uprising and subsequent Indian crackdown.
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