However, bypolls in two Assembly constituencies each in Karnataka and Madhya Pradesh, one each in West Bengal, Assam, Rajasthan and Delhi passed off peacefully.
In all, by-elections were held in eight Assembly constituencies in five states, besides the Srinagar parliamentary seat.
Stone-pelting was reported from over two dozen places across the three districts of Srinagar, Budgam and Ganderbal which constitute the Srinagar constituency. The main contestants for the seat are Farooq Abdullah, the joint candidate of the National Conference and the Congress, and Nazir Ahmad Khan, the ruling PDP's nominee.
More than 100 security force personnel were injured in the violence, officials said, adding that several civilians were also injured in police firing.
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J-K Chief Electoral Officer Shantmanu said a poor 6.5 per cent polling took place in the parliamentary seat.
"I cannot say anything about the repoll as of now. The figure can be anywhere around 50 or 100 polling stations or more than that," he told reporters.
While two persons each were killed Pakherpora in Chrar-e- Sharief and Beerwah areas of Budgam district, one death was reported from Chadoora area of the same district and another in Magam town, which is known as the gateway to Gulmarg.
Firing incidents were also reported from at two places in Madhya Pradesh after Congress and BJP workers clashed during the by-election in Ater Assembly seat.
The MP election commission, however, dismissed reports of booth capturing and said security was tightened after the incidents.
In Dholpur Assembly constitituency in Rajasthan, where BJP is in power, 74 per cent polling was recorded till 5 PM.
BJP-ruled Assam's Dhemaji seat had a turnout of 66.97 per cent while it was 65 per cent in Bandhavgarh and 60 per cent in Ater in MP where BJP is in office.
The turnout in Kanthi Dakshin Assembly seat in TMC-ruled West Bengal was 79.7 per cent till 5 PM while it was 44 per cent in Delhi's Rajouri Garden Assembly seat till that time. AAP holds office in Delhi.
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