The violence erupted on Thursday when Uttarakhand state officials moved to demolish a property that an official said was neither registered as a madrasa nor as a place to offer Islamic prayers, though some locals considered it a religious site.
"I can confirm two have lost their lives and three people are serious (injured)," said senior police official Prahlad Narayan Meena. "Over 80 suffered injuries due to stone pelting, including some police and reporters."
Vandana, the district magistrate of Nainital where Haldwani is located, told a press conference the demolition drive and its aftermath were "not communal and should not be seen as such".
The officer, who goes by one name, said the protests were linked to the government drive to demolish a "property that is neither registered as religious site nor has it been given any such recognition. Some call the structure a madrasa".
Sumit Hridayesh, a state lawmaker from the opposition Congress party who represents Haldwani, said the violence was a result of "hasty action" by the administration. He said locals of the area, including Muslim clerics, should have been taken into confidence before starting the drive.
Uttarakhand's chief minister, Pushkar Singh Dhami, said the government would take the "strictest action against rioters and miscreants".
"Police have been given clear instructions to deal strictly with unruly elements," he said in a statement. "Every rioter who indulged in arson and stone pelting is being identified. No miscreant who disturbs harmony and peace will be spared."
Haldwani is under curfew for a second day.
