Article published on the 2008-11-03 Latest update 2008-11-03 15:00 TU
"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, according to the state-run Associated Press of Pakistan. "It is creating a credibility gap."
It is the highest-level protest against continuing attacks by unmanned US aircraft, which have sparked angry protests after allegedly killing dozens of civilians.
Earlier, Defence Minister Chaudhry Ahmad Mukhtar delivered the same message at a meeting with Petraeus, Assistant Secretary of State Richard Boucher and ambassador Anne Patterson.
"The frequent drone attacks could lead to generate anti-America sentiments as well as create outrage and uproar among the people," Mukhtar's department said in a statement.
Islamabad has repeatedly protested about the air-strikes, which Washington has never officially accepted responsibility for, with national security adviser Mahmud Ali Durrani protesting in person to White House officials.
But they continue, with two separate strikes in North and South Waziristan which Pakistani officials say killed 32 people, mainly Al-Qaeda operatives.
The political and security situation in Pakistan and its effect on Afghanistan, have become an issue in the US election debate, with Democrat Barack Obama declaring that he would openly attack Pakistani territory if US security required such action.
Petraeus' visit so early in his mandate shows the importance of the country to current US strategy, says correspondent Rana Jawad.
He says that the talks also covered proposals to change Islamabad's strategy.
"The latest innovation that Pakistan is going to adopt in its fight against terrorism is strengthening the paramilitary troops," he told RFI. "And that we believe is the idea of the new Centcom [United States Central Command] chief. He wants paramilitary forces to be trained by the US and be in frontline of the war on terror."