Members of the hardline Vishwa Hindu Parishad (VHP) stormed the set in the northern-Indian city of Chandigarh, where Bigelow's crew had been shooting for four days.
The location was a market, which the production company had transformed with shopboard signs in Urdu, autorickshaws with Lahore number plates and burqa-clad extras.
"They removed signs that had been put up in Urdu and also pushed and abused the camera crew. They raised slogans against Pakistan and forcibly removed some Pakistani flags," said a local police officer.
"We don't want Pakistani flags on Indian soil and we don't agree that Indian markets should look like Pakistan," said VHP secretary Ramkrishna Srivastava.
Under the working title Zero Dark Thirty, Bigelow's latest film recounts the hunt for Bin Laden, which ended when US special forces raided his hideout in the Pakistani garrison town of Abbottabad last May, killing the Al-Qaeda leader.
With filming in Pakistan not an option, there has been intense media speculation about what locations might be chosen by Bigelow, who won the 2010 Oscar for Best Director for The Hurt Locker.
Indian newspaper reports had suggested she might look to recreate the recently demolished three-storey Bin Laden hideout in the desert state of Rajasthan.
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