Panetta said he knows of no other senior U.S. military officers being linked to the Petraeus investigation, and he said he retains "tremendous confidence" in Allen.
"I am not aware of any others that could be involved in this issue at the present time," he said, adding that he wanted the American public to understand that the vast majority of military officers serve ethically.
"One thing I do demand," he said, "is that those who seek to protect this country operate by the highest ethical standards."
Panetta declined to describe the nature of the emails and other correspondence between Allen and Florida socialite Jill Kelley, which others have called flirtatious and potentially problematic for the Marine four-star general.
Asked whether any of those emails are sexually explicit, Panetta said, "What I don't want to do is to try to characterize those communications because I don't want to do anything" to limit the ability of the Pentagon inspector general to conduct an objective review of the Allen matter.
Panetta ordered the investigation Monday after the FBI referred the matter to the Pentagon's top lawyer. Allen issued a statement through his lawyer saying he is committed to cooperating fully with the investigation.
Panetta also told reporters he could not rule out the possibility that the Taliban in Afghanistan would try to use Petraeus' admission of an extramarital affair with his biographer, Paula Broadwell, for propaganda purposes. Petraeus, who resigned Friday from his post as CIA director, was Allen's predecessor as top commander in Afghanistan, leaving in summer 2011.
"You're never quite sure what the Taliban may or may not use for propaganda purposes to try to advance their cause, and obviously this is a possible area for them to explore," Panetta said, adding that "if they want to have an impact" there are other issues they could try to exploit.
Panetta is the first U.S. defense secretary to visit Thailand since 2008. The U.S. has no troops permanently stationed in Thailand but it conducts regular exercises with the Thai military and has numerous other forms of cooperation.