Allen, 58, insisted he'd done nothing wrong and worked to save his imperiled career.
Kelley, 37, who had worked herself into the center of the military social scene in Florida without having any official role, emerged as a central figure in the still-unfolding story that has embroiled two of the nation's most influential and respected military leaders.
Known as a close friend of retired Gen. Petraeus, Kelley triggered the FBI investigation that led to his downfall as CIA director when she complained about getting anonymous, harassing e-mails. They turned out to have been written by Petraeus' mistress, Paula Broadwell, who apparently was jealous of the attention the general paid to Kelley. Petraeus acknowledged the affair and resigned Friday.
In the course of looking into that situation, federal investigators came across what a Pentagon official called "inappropriate communications" between Allen and Kelley, both of them married.
According to one senior U.S. official, the e-mails between Allen and Kelley were not sexually explicit or seductive but included pet names such as sweetheart or dear. The official said that while much of the communication - including some from Allen to Kelley - is relatively innocuous, some could be construed as unprofessional and would cause a reasonable person to take notice.
That official, as well as others who described the investigation, requested anonymity on grounds that they were not authorized to discuss the situation publicly.
The FBI decided to turn over the Allen information to the military once the bureau recognized it contained no evidence of a federal crime, according to a federal law enforcement official, who was not authorized to discuss the matter on the record and demanded anonymity. Adultery, however, is a crime under the Uniform Code of Military Justice.
A senior defense official said that the FBI first notified the Pentagon of the Allen matter Sunday afternoon. The Pentagon's top lawyer called Defense Secretary Leon Panetta's chief of staff, Jeremy Bash, about 5 p.m. as Bash and Panetta were flying to Honolulu to begin a weeklong Asia trip. Bash then informed Panetta.
Allen was not suspended from his military position, even though his nomination for promotion is on hold. Kelley served as a sort of social ambassador for U.S. Central Command in Tampa, hosting parties for Petraeus when he was commander there from 2008 to 2010.
The friendship with the Petraeuses began when they arrived in Tampa and the Kelleys threw a welcome party at their home, a short distance from Central Command headquarters, introducing the new chief and his wife, Holly, to Tampa's elite, according to staffers who served with Petraeus.
White House spokesman Jay Carney, employing understatement, was asked about the revelations involving Allen and said Obama "wouldn't call it welcome" news. Carney described Obama as "surprised" by the earlier news about Petraeus.