Police fired teargas at stone-throwing protesters in Srinagar on Saturday while shops stayed shut after separatists called a strike to protest against a visit by President Pratibha Patil.
Patil, who became India's first female president last year, began her five-day tour on Friday to Kashmir, a region wracked by nearly 20-years of bloody revolt against Indian rule.
Streets in Kashmir's summer capital were largely deserted except for patrols by a larger than usual number of police and soldiers.
The strike was called by prominent hardline separatist Syed Ali Shah Geelani and backed by a Pakistan-based alliance of Kashmiri militants called the United Jihad Council.
"We appeal to people to observe a complete strike on Saturday to protest against Indian president's visit," Geelani said. "The strike would be a mark of protest against the Indian occupation of Kashmir."
While most people stayed indoors, around 150 protesters gathered in the streets, threw stones and shouted slogans before police fired tear gas.
"We want freedom. Indian troops go back," the protesters shouted.
Officials say more than 43,000 people have been killed in violence between separatist guerrillas and Indian troops since 1989. Human rights groups put the toll at around 60,000 dead or missing.
Officials say rebel violence is waning after India and Pakistan, who claim the scenic region in full and have fought wars over it, began a slow-moving peace process in 2004.
"I am glad that after a difficult period Jammu and Kashmir is progressing well on the road to development and peace," Patil said in a speech at the Sher-i-Kashmir Institute of Medical Sciences in Srinagar on Friday.
Patil addressed Indian troops on Friday and visited a military control line dividing Kashmir between India and Pakistan.