Infidelity or national security crisis as saga of deposed CIA chieftain GEN. DAVID PETRAEUS continues unabated as federal agents raid PAULA BROADWELL’s home. SEE VIDEO

And now, Pentagon officials confirm that the U.S.'s commander highest-ranked in Afghanistan, Gen. John Allen, is ALSO under investigation in connection to the ongoing scandal.

Hunting for top secret docs, federal agents late Monday raided Broadwell's Charlotte, North Carolina home, FBI spokeswoman Shelley Lynch said, to execute a search her lawyers had previously consented to.

 FBI agents departed with cardboard boxes after snapping pictures of the house.

Defense Secretary Leon Panetta says he ordered the Pentagon to investigate claims Allen — a four-star Marine general — had "potentially inappropriate communications" with Jill Kelley, who purportedly received threatening e-mails from Broadwell, RadarOnline.com reported.

Kelley, 37, promptly released statement requesting privacy for her family, adding they've been friends with Petraeus (who has denied cheating with anyone other his biographer Broadwell) for years.

A military official — noting that between 20,000 to 30,000 pages of email and other writings from Allen’s communications with Kelley between 2010 and 2012 were collected in the investigation and are under review — told the AP under conditions of anonymity that "Gen. Allen disputes that he has engaged in any wrong doing in this matter.

"We'll have to let the process follow its course. As I said, and you'll see in the Secretary's statement, we believe that General Allen is entitled to due process. We need to see where the facts lead in this matter before jumping to any conclusions whatsoever."

The official said investigators are "in the very early stages of reviewing the documents right now," and that the matter has been referred to the [Inspector General], the IG will do a thorough investigation of the documents."

Allen, who took over Petraeus' top spot in July 2011, will remain stationed in Kabul commanding the International Security Assistance Force, Panetta said.

As The ENQUIRER reported previously, Petraeus, 60, quit as CIA director last week, citing his extramarital affair with Broadwell, his stunning 40-year-old biographer, as the reason.