A senior US military official is under investigation for alleged inappropriate communication with a woman at the centre of the scandal involving former CIA director David Petraeus.
The FBI is reported to have uncovered thousands of pages of communications between General John Allen and Jill Kelley, who has been identified as a long-time friend of the Petraeus family.
Gen Allen is the top US commander in Afghanistan and was due to be nominated to a senior position in the US European Command.
It was Ms Kelley's complaints about harassing emails from the woman with whom Mr Petraeus had an affair, Paula Broadwell, that prompted an FBI investigation.
The inquiry ultimately alerted authorities to Mr Petraeus' involvement with Ms Broadwell.
Mr Petraeus resigned from his job on Friday.
Asked whether there was concern about the disclosure of classified information, the official, on condition of anonymity, 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 Gen Allen's nomination to be Commander of US European Command and Supreme Allied Commander Europe be delayed "and the president has agreed".
Gen 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 Mr Panetta directed the Defense Department's Inspector General to handle the investigation.
Gen Allen has denied any wrongdoing.
Earlier, Mr Panetta had said he was reviewing Gen Allen's recommendations on the future US presence in Afghanistan after most troops withdraw by the end of 2014.
Evidence that the case involving Mr Petraeus was not fully closed came yesterday when FBI agents searched the Charlotte, North Carolina, house of Ms Broadwell.
Agents entered the house at around 9pm (2am Irish time) and about four hours later took away what appeared to be two computers and about ten boxes.
Ms Broadwell's family was not at home at the time of the raid.