Police detained three separatist leaders to try to stop the protests. Troops enforced a curfew in the summer capital of Srinagar, where a separatist rally had been planned, and armoured vehicles patrolled mainly deserted streets.
But thousands of Muslim protesters shouting "we want freedom" defied the curfew in about a dozen rural areas.
Four protesters were killed and at least 80 people were wounded when police fired bullets and tear gas, the police said.
Police have killed at least 27 protesters and more than 500 have been wounded in clashes in two weeks of demonstrations in the Kashmir Valley over a land dispute between Muslims and Hindus.
The crisis has strained relations between India and Pakistan, which both claim the region but rule it in parts. It has also raised fears of tension in the state, split between the Hindu-majority Jammu region and the Muslim Kashmir Valley.
Police said Mirwaiz Umar Farooq, chairman of Kashmir's main separatist alliance, All Parties Hurriyat (Freedom) Conference, and hardliner Syed Ali Shah Geelani were detained in overnight raids in Srinagar.
"Both have been detained for precautionary measures," said a senior police official, who declined to be named.
Another separatist leader, Mohammed Yasin Malik, chief of Jammu Kashmir Liberation Front, was detained later on Monday after he broke the curfew, police said.
"The people of Kashmir were ready to defy the curfew and carry out the march to protest against Indian occupation," a statement from the All Parties Hurriyat Conference said.
Dozens Injured
One person was killed and dozens were injured on Sunday when police fired bullets and tear gas and used batons to disperse thousands of pro-independence protesters defying the curfew.
The recent crisis began after the state government promised to give forest land to a trust that runs Amarnath, a cave shrine visited by Hindu pilgrims. Many Muslims were enraged.
The government then rescinded its decision, which in turn angered Hindus in Jammu, the winter capital of the region.
In Jammu, around 25 Hindu protesters were wounded on Monday in clashes with police as authorities enforced a curfew on the highway town of Kathua, police said.
A strike in Jammu called by Hindu groups has shut many businesses for the past month.
The conflict has had little impact on national politics, with a consensus in India that Kashmir should stay part of the country, no matter what.
With a general election approaching early next year, political analysts say there is little chance of Prime Minister Manmohan Singh giving any concessions to the protesters, with the government hoping that the demonstrations will peter out.
Most separatist groups seek the implementation of U.N. resolutions from 1948 for a plebiscite to decide on the future of the region. But the India government rejects a plebiscite.
In Kashmir, officials say more than 43,000 people have been killed in violence involving Indian troops and Muslim militants since 1989. Human rights groups put the toll at about 60,000 dead or missing.
Levels of violence in Kashmir have been falling in the past few years amid tighter Indian security and a tentative peace process between Pakistan and India.
