In a dispatch from Washington, The New York Times, citing a senior US official, said Khalilzad was facing angry questions from other senior Bush administration officials over his phone calls to Zardari several times a week in the past month until he was confronted.
Other officials said Khalilzad had planned to meet Zardari privately next Tuesday while on vacations in Dubai, in a session that was cancelled only after Richard Boucher, the assistant secretary of state for South Asia, learned from Zardari himself that the Ambassador was providing "advice and help."
"Can I ask what sort of 'advice and help' you are providing?" Boucher wrote in an angry e-mail message to Khalilzad, according to The Times.
"What sort of channel is this? Governmental, private, personnel?" Copies of the message were sent to others at the highest levels of the State Department.
The Times said Boucher's message was provided to it by an administration official who had received a copy.
"Officially, the US has remained neutral in the contest to succeed Mr Musharraf, and there is concern within the State Department that the discussions between Mr Khalilzad and Mr Zardari, the widower of Benazir Bhutto, a former prime minister, could leave the impression that the US is taking sides in Pakistan's already chaotic internal politics," the dispatch said.
"Mr Khalilzad also had a close relationship with Ms Bhutto, flying with her last summer on a private jet to a policy gathering in Aspen, Colorado."
"The conduct by Mr Khalilzad has also raised hackles because of speculation that he might seek to succeed Hamid Karzai as president of Afghanistan. Mr Khalilzad, who was the Bush administration's first Ambassador to Afghanistan, has also kept in close contact with Afghan officials, angering William Wood, the current American Ambassador, said officials, who spoke on condition of anonymity because they were not authorised to speak publicly on the matter of Khalilzad's contacts.
Khalilzad has said he has no plans to seek the Afghan presidency." through his spokesman, he said he had been friends with Zardari for years.
"Ambassador Khalilzad had planned to meet Zardari socially during his personal vacations," Richard Grenell, the spokesman for the US Mission to the United Nations, was quoted as saying.
"But because Zardari is now a presidential candidate, Ambassador Khalilzad postponed the meeting, after consulting with senior State Department officials and Zardari himself."
A senior American official said that Khalilzad had been advised to "stop speaking freely" to Zardari, and that it was not clear whether he would face any disciplinary action.
According to The Times, Administration officials described John Negroponte, the deputy secretary of state, and Boucher as angry over the conduct of Khalilzad because as UN Ambassador he has no direct responsibility for American relations with Pakistan.
Those dealings have been handled principally by Negroponte, Boucher and Anne Patterson, the American Ambassador to Pakistan.
"Why do I have to learn about this from Asif after it's all set up?" Boucher wrote in the Aug 18 message, referring to the planned Dubai meeting with the PPP leader.
"We have maintained a public line that we are not involved in the politics or the details. We are merely keeping in touch with the parties. Can I say that honestly if you're providing 'advice and help'? Please advise and help me so that I understand what's going on here."
This is not the first time Khalilzad got into trouble for unauthorised contacts. In January, White House officials expressed anger about an unauthorised appearance in which Khalilzad sat beside the Iranian foreign minister at a panel of the World Economic Forum in Davos, Switzerland.
The US does not have diplomatic ties with Iran, and a request from Khalilzad to be part of the US delegation to Davos had been turned down by officials at the State Department and the White House, a senior administration official said.
"I know that Zardari's interest in becoming president has been clear for quite some time," Teresita C Schaffer, a Pakistan expert at the Center for Strategic and International Studies in Washington, was quoted as saying.
The Bush administration has long been uneasy with the idea of Nawaz Sharif as a potential leader of Pakistan, and now that Musharraf is out of the picture, the administration, despite public protestation of neutrality, is seeking another ally, The Times said.
"It distresses me that the US government has not learned yet that having 'our guy' is not a winning strategy in Pakistan," Ms Schaffer said.
"Whoever 'our guy' is isn't going to be the only guy in town, and if we go into it with that view, we'll bump up against a lot of other guys in Pakistan."
An unnamed senior Pakistani official was quoted as saying that the relationship between Khalilzad and Zardari went back several years, and that the men developed a friendship while Zardari was spending time in New York.
The Pakistani official said the consultations between the men were an open exchange of information, with each one giving insight into the political landscape in his capital.
"Mr Khalilzad, being a political animal, understood the value of reaching out to Pakistan's political leadership long before the bureaucrats at the State Department realised this would be useful at a future date," the official said. The Ambassador "did not make policy or change policy, he just became an alternate channel," the official said.
Of Khalilzad's Pakistan contacts, Sean McCormack, the State Department spokesman said, "Our very clear policy is that the Pakistanis have to work out any domestic political questions for themselves." Gordon Johndroe, a White House spokesman, said, "The Pakistani elections are an internal matter for the Pakistani people."