Police used teargas and batons to disperse hundreds of stone-throwing demonstrators shouting, "We want freedom," and "La ilaha illalah" (There is no god, but Allah) in several parts of Kashmir.
A police officer was seriously wounded when suspected militants attacked police posts with grenades in north Kashmir on Friday, police said. They said three militants had been killed in gunbattles with soldiers since Thursday.
Police and soldiers in riot gear patrolled other deserted streets in Srinagar, the capital of the mainly Muslim Kashmir Valley, and warned residents to stay indoors.
Indian authorities have deployed thousands of troops in Srinagar, enforcing an undeclared curfew, to thwart planned anti-election protests.
"We are sick and tired of this, every second day they impose a curfew," said Tania Khan, 27-year-old bank employee.
"Life is miserable here."
Life in Srinagar has been frequently disrupted by strikes, demonstrations and curfews, especially since some of the biggest anti-India protests in years erupted several months ago. At least 42 people were killed by security forces during those protests.
Separatists had planned more protests on Friday to renew their appeal for a boycott of the seven-stage, month-long vote.
The authorities, buoyed by a decent turnout in the first round of the vote on Monday, blocked the move. Many separatist leaders remain in jail or under house arrest.
The second phase of voting is on Sunday.
Srinagar will vote in the seventh and final phase. It will be the third election in the state since an insurgency began in 1989, killing at least 47,000 people.
"We appeal to people to stage peaceful protests against the holding of elections in the presence of 700,000 troops and against the arrest of leaders," said a statement of the Jammu-Kashmir Coordination Committee, a new alliance of Muslim separatists, business people and lawyers.
Shops, businesses and schools were also closed in other towns across the Kashmir Valley.
In the past, separatist guerrillas have attacked and killed scores of candidates and political workers, vandalised polling stations and attacked rallies to thwart elections.
But early this year, the United Jihad Council, a Pakistan-based militant alliance fighting Indian troops in Kashmir, rejected the use of violence to enforce a boycott.
Violence has declined significantly since India and Pakistan, which both claim the region in full and rule in part, began a slow-moving peace process in 2004.
