Zardari is close to the United States and had earlier promised to maintain nuclear-armed Pakistan's commitment to the U.S.-led "war on terrorism," even though it is deeply unpopular.
The United States and Afghanistan say al Qaeda and Taliban militants operate out of sanctuaries in remote ethnic Pashtun lands on the Pakistani side of the Afghan border.
Frustrated by an intensifying Taliban insurgency in Afghanistan, the United States has stepped up attacks on militants in Pakistan with six missile attacks and a helicopter-borne ground assault this month.
The army has vowed to stand up to aggression across the border. But a senior Pakistani official told Reuters earlier the latest missile strike, which killed five militants on Wednesday, was the result of better U.S.-Pakistani intelligence-sharing.
Zardari did not refer specifically to the United States but said territorial violations were unacceptable.
"We will not tolerate the violation of our sovereignty and territorial integrity by any power in the name of combating terrorism," Zardari told parliament.
Now if we can just get them to stop offering "political support to what it calls a freedom struggle in Indian Kashmir."