The shocking revelation threatens to fell General John Allen, another of the US military's biggest names, and suggests that the scandal involving Petraeus - a former four-star general who had John Allen's job in Afghanistan before moving to the CIA last year - could expand much further than previously imagined.
The US official said the FBI uncovered between 20,000 and 30,000 pages of communications - mostly emails and spanning from 2010 to 2012 - between Allen and Jill Kelley, who has been identified as a long-time friend of the Petraeus family and a Tampa, Florida, volunteer social liaison with military families at MacDill Air Force Base.
It was Kelley's complaints about harassing emails from the woman with whom Petraeus had had an affair, Paula Broadwell, that prompted an FBI investigation, ultimately alerting authorities to Petraeus' involvement with Broadwell. Petraeus resigned from his job on Friday.
Asked whether there was concern about the disclosure of classified information, a US defence official said: "We are concerned about inappropriate communications. We are not going to speculate as to what is contained in these documents."
Defence Secretary Leon Panetta said he had asked that Allen's nomination to be Commander of US European Command and Supreme Allied Commander Europe be delayed "and the president has agreed".
Allen, who is now in Washington, was due to face a Senate confirmation hearing on Thursday, as was his slated successor in Afghanistan, General Joseph Dunford.
The FBI referred the case to the Pentagon on Sunday and Panetta directed the Defence Department's Inspector General to handle the investigation. Panetta informed the top Republican and Democrat on the Senate Armed Services Committee during the flight to Australia. The House Armed Services Committee was also notified.
The US defence official said that Allen denied any wrongdoing and that Panetta had opted to keep him in his job while the matter was under review, and until Dunford can be confirmed to replace him - a process that gains urgency given the potentially lengthy review process and the cloud it could cast over the mission in Afghanistan.
"While the matter is under investigation and before the facts are determined, General Allen will remain commander of ISAF," Panetta said, referring to the NATO-led force in Afghanistan.
Only hours earlier, Panetta had said he was reviewing Allen's recommendations on the future US presence in Afghanistan after most troops withdraw by the end of 2014.
Commending Allen's leadership in Afghanistan, Panetta said in his statement: "He is entitled to due process in this matter."
At the same time, he noted that he wanted the Senate to act "promptly" on Dunford's nomination.
The US official said Panetta was informed of the matter involving Allen on Sunday, as he flew to Hawaii, after the Pentagon's top lawyer called Panetta's chief of staff. The White House was informed next.
Evidence that the case involving Petraeus was not fully closed came late last night when FBI agents searched the Charlotte, North Carolina house of Broadwell.
Agents entered the house carrying boxes and about four hours later took away what appeared to be two computers and about 10 boxes.
During the search, agents inside could be seen moving through multiple rooms, gathering materials and taking photos. They did not comment to reporters gathered outside the house.
Broadwell's family was not at home at the time of the raid. The FBI and a Justice Department official would not comment on the reason for the raid.
US officials had said in recent days that their investigation was largely complete and that prosecutors had determined it was unlikely they would bring charges in that case, which started when Kelley contacted an FBI agent in Tampa about harassing emails from an anonymous source.
That FBI agent, who has not been identified, has also come under scrutiny after it was discovered he had sent shirtless photographs of himself to Kelley, but "long before" this investigation, a law enforcement official said. The photographs were first reported by the Wall Street Journal.
The agent had never been on the Broadwell case, but had taken the information about the emails to the FBI cyber squad in Tampa, the law enforcement official said.
The FBI agent who works in the Tampa office apparently became frustrated at the pace of the investigation and complained to a member of Congress about it, the official said.
The FBI investigation of the emails received by Kelley traced them to Broadwell and subsequently uncovered emails that revealed an affair between Broadwell and Petraeus.
The emails between the two women were of a "childish", jealous nature and showed some one-upmanship of trying to come across as being more important to Petraeus, the official said.
When Petraeus resigned as CIA director on Friday he publicly admitted to having engaged in an extramarital affair.
Lawmakers and others have questioned whether Broadwell, who co-wrote a biography of the decorated former general, obtained classified information from him or another source.
Panetta had earlier said Petraeus did the right thing by stepping down, given potential security concerns, even as he said he was saddened by the end of the retired general's distinguished career.