PERTH, Australia (Reuters) - U.S. Defense Secretary Leon Panetta warned on Wednesday against jumping to conclusions over the actions of the top U.S. commander in Afghanistan, a day after placing him under investigation in a widening scandal that already cost CIA Director David Petraeus his job.

Marine General John Allen, who denies any wrongdoing, is being investigated for potentially inappropriate communications with a woman at the center of the Petraeus case, Jill Kelley, a Florida socialite.

Panetta defended his decision to refer the case to the Pentagon's inspector general and for suspending Allen's nomination to another top position in the U.S. military, saying it was a prudent step "until we determine what the facts are."

"And we will," Panetta told reporters at high-level talks in Australia, also attended by the top U.S. military officer, General Martin Dempsey, and Secretary of State Hillary Clinton.

At the same time, he praised Allen's work commanding the Afghan war effort, a position he retains despite the probe.

"No one should leap to any conclusions here. General Allen is doing an excellent job at ISAF, in leading those forces," Panetta said, referring to the NATO-led force.

"He certainly has my continued confidence to lead our forces and continue the fight."

Clinton acknowledged that allies had raised questions about the Allen case but said there was "no concern whatsoever being expressed to us" about the mission in Afghanistan.

Defense officials and people close to Petraeus say neither he nor Allen had a romantic relationship with Kelley, a 37-year-old wife and mother, who is described as a prominent presence in military circles in Tampa.

She may have been seen as a rival by Petraeus' biographer, Paula Broadwell, who sent Kelley a series of anonymous, harassing emails which touched off an investigation that uncovered evidence of an affair between Petraeus and Broadwell.

According to law enforcement sources, FBI investigators decided to pursue the matter when they found the messages contained information about the CIA chief's activities that was not publicly available.

Kelley had gotten to know both Petraeus and Allen as a volunteer setting up social events at MacDill Air Force Base outside Tampa, headquarters of U.S. Central Command.

The relationship was evidently close enough that both men intervened in a child custody battle involving Kelley's twin sister, Natalie Khawam.

"She is a dedicated mother, whose only focus is to provide the necessary support, love, and care for her son," Allen wrote about Khawam in a September 22 letter to a Washington, D.C., court.

Allen and Kelley communicated often enough over the past two years to produce between 20,000 and 30,000 pages of email and other messages, which were turned over to Defense Department investigators on Sunday.

The actual volume of communications is likely much smaller, an official said, as the printouts include messages involving other people and email threads including prior communications.

A senior defense official told Reuters the messages were seen as inappropriate because they were "flirtatious" in nature, not because they dealt with sensitive information.

But "flirtatious" may be an understatement. Another U.S. official said the Pentagon only decided to refer it for investigation after an initial look found the communications to be of "a sufficient character" to warrant further review.

Allen has denied that the two had a sexual relationship, officials said on condition of anonymity. Adultery can lead to a dishonorable discharge under U.S. military law.

WHITE HOUSE BACKS ALLEN

The scandal complicates President Barack Obama's efforts to reorganize his national security team following his re-election. The White House said it still had faith in Allen, but acknowledged its plans to transfer him to Europe, where he would head U.S. and allied forces, have been suspended.

Obama also has to find a replacement for Petraeus at the CIA at a time when the president is vetting candidates to head the State and Defense departments.

The scandal could throw a wrench into Obama's relations with Congress at a time when he is engaging in high-stakes budget negotiations to avoid the combination of tax increases and spending cuts known as the "fiscal cliff."

"I certainly wouldn't call it welcome," White House spokesman Jay Carney said of the scandal.

Both Allen and the official due to replace him in Afghanistan, Marine Corps General Joseph Dunford, must be confirmed by the U.S. Senate before they can take up their new posts.

Lawmakers on the Senate Armed Services Committee said they would go ahead with a confirmation hearing for Dunford on Thursday. Allen's appearance was canceled.

Allen had just submitted recommendations on what role the United States should play in Afghanistan after most American combat troops withdraw by the end of 2014.

FBI agents searched Broadwell's Charlotte, North Carolina, home late on Monday in a sign that the case involving Petraeus was not fully closed.

Agents entered the house carrying boxes at around 9 p.m. (0200 GMT Tuesday) and emerged four hours later, carrying away what appeared to be two computers and about 10 boxes.

Broadwell's family was not at home at the time.

U.S. officials have said recently 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.

That FBI agent, who has not been identified, came under scrutiny himself after it was discovered he had sent shirtless photographs of himself to Kelley "long before" this investigation, a law enforcement official told Reuters.

The agent, who alerted an FBI cyber squad to the Broadwell case, apparently became frustrated at the pace of the investigation and complained to a member of Congress about it, the official said.