Pakistani officials say troops exchanged fire with the chopper, and two soldiers were wounded in the Datta Khel area of the North Waziristan tribal region, a known sanctuary for Taliban and al Qaeda militants.
NATO is confirming there was a firing, but did not confirm any Pakistani troops were hit. NATO said it was still trying to determine whether the helicopter crossed in to Pakistani airspace.
Many American lawmakers have said bin Laden's location was a strong sign that Pakistan was playing a "double game" - that is accepting U.S. aid but also protecting terrorists. Pakistan denies that.
The Pakistani army, facing internal criticism for failing to detect or stop the unilateral American raid that killed bin Laden, said it lodged a strong protest and demanded a meeting with NATO officials to discuss the incident. NATO said it would investigate.
The Pakistani government is outraged that the U.S. carried out the operation without telling Pakistan first, and many U.S. officials have expressed disbelief that bin Laden could have lived in Abbottabad for at least five years without the authorities' knowledge.
The Associated Press contributed to this report.