Petraeus, who now oversees the wars in Afghanistan and Iraq, told CNN he had heard criticism over the U.S. attacks on militant targets on the Pakistani side of the border with Afghanistan.
"In fact, we got certain messages with each of those we talked today and some of those were very clear and we have to take those on board," CNN quoted Petraeus as saying. "The tone of the conversation was very frank and very forthright, as it should be," he added later.
There is growing U.S. concern about how Islamic militants are using pockets of Pakistan's northwest region as sanctuaries to support the escalating insurgency in Afghanistan.
Complaints from U.S. commanders about Pakistan's efforts to counter the insurgents have been accompanied by a surge of missile strikes on suspected Taliban and al-Qaida targets, despite condemnation in Pakistan.
According to state-run APP news agency, Zardari told Petraeus and Assistant Secretary of State Richard Boucher that the attacks from unmanned drones should be stopped. Washington is suspected of launching at least 17 such missile strikes on Pakistan since August.
"Continuing drone attacks on our territory, which result in loss of precious lives and property, are counterproductive and difficult to explain by a democratically elected government," Zardari was quoted as saying.
He said the government was "under pressure to react more aggressively" to the strikes.
In September, a U.S. ground assault in a tribal region in Pakistan's northwest spurred particular outrage. Days later, Pakistani troops fired on or sent flares at two American helicopters operating near the border and U.S. and Pakistani ground forces in the area exchanged fire.
There have been no reports of additional ground assaults since and Petraeus has given few hints about what strategy he will follow.
Without confirming the subject of Petraeus' discussions in Pakistan, White House press secretary Dana Perino said it is normal for allies such as the U.S. and Pakistan to exchange views frankly.
"There's a lot of tension in Pakistan right now," Perino said. "They have a lot of issues on their plate, from terrorists to their economy to the concerns about their future security and their political situation, as they have a new administration that's trying to get settled."
Pakistan's government is mindful of widespread opposition at home to its ties with Washington. However, it has acknowledged its dependence on Western aid in the face of economic problems and taken a tough public stance against terrorism and extremism.
Defense Minister Ahmad Mukhtar said in a statement after his meeting with Petraeus that missile strikes could "create outrage and uproar among the people." But his statement also noted that both sides "stressed the need for enhanced cooperation to eliminate the scourge of terrorism."
It was unclear whether Petraeus addressed vows from Pakistani and Afghan leaders to seek talks with elements of the Taliban. Petraeus, previously the top U.S. commander in Iraq, has indicated support for efforts to reach out to members of the Taliban considered moderate enough to cooperate with the Afghan government.
Petraeus' visit came on the eve of U.S. presidential elections. Democratic candidate Barack Obama has said if he is elected, he could launch unilateral attacks on high-value terrorist targets in Pakistan as they become exposed and "if Pakistan cannot or will not act" against them. Republican rival John McCain says engaging Pakistanis is vital to defeating extremists, and that cross-border strikes shouldn't be discussed "out loud."