State and paramilitary police fired bullets and shotgun pellets as thousands of protesters shouting slogans against Indian rule charged into voting booths in Budgam district near the main city of Srinagar.
"Violent protests happened at many places in Budgam. Protesters damaged and snatched EVMs (electronic voting machines) at some places," Shantmanu, the state's chief electoral officer, told AFP.
"It was not a good day for all of us. Six civilians were killed and 70 were wounded," Shantmanu, who uses only one name, told reporters.
Many were grievously injured with bullets fired by police and paramilitary troops, hospital sources in Srinagar said.
The electoral officer said more than 100 government personnel, including police and paramilitary officers were also injured in the clashes.
In the Charare-e-Sharif area of Budgam two people were killed when the paramilitary Border Security Force fired at protesters, he said.
Another person was killed in the Beerwah area of the same district when paramilitary police opened fire at a stone-throwing crowd.
Three more were killed in the day-long clashes, with two of them succumbing to multiple pellet injuries from the shotguns which Indian paramilitary forces use in Kashmir for crowd control.
Polling had to be halted in more than dozen places amid a call by top Kashmiri separatist leaders opposed to Indian rule to boycott the by-election.
Only 6.5 percent of voters turned out to cast their ballot, Shantmanu said, 26 percent less than in the last elections held in 2014 and the lowest ever participation recorded in any election in the disputed territory.
- Internet suspended -
Former state chief minister Farooq Abdullah, who is contesting the Srinagar seat, slammed the government for its failure to maintain law and order.
"Elections should have been peaceful. This government has failed in giving a peaceful atmosphere for people to come and vote," he told reporters.
Ahead of the polling, authorities suspended internet services across the Kashmir Valley for fear of widespread protests.
Police had also detained hundreds of young people and separatist activists in the run-up to the poll, sources told AFP.
Kashmir has been divided between India and Pakistan since the end of British rule in 1947. Both claim the disputed territory in its entirety.
Rebel groups in Indian Kashmir have for decades battled troops and police, demanding independence or a merger of the territory with Pakistan.
Around 500,000 Indian soldiers are deployed in the region.
Ahead of Sunday's polling, the Indian government had sent in 20,000 additional paramilitaries.
Armed encounters between rebels and government forces have become more frequent since the killing of a popular rebel leader by security forces last July sparked widespread unrest.
Police and army officials say dozens of local youths have joined the rebel ranks since then.
At least 29 armed militants, mostly locals, have died fighting government forces this year.