A senior official confirms to Fox News that the conduct of Sgt. Bowe Bergdahl -- both in his final stretch of active duty in Afghanistan and then, too, during his time when he lived among the Taliban -- has been thoroughly investigated by the U.S. intelligence community and is the subject of "a major classified file."

In conveying as much, the Defense Department source confirmed to Fox News that many within the intelligence community harbor serious outstanding concerns not only that Bergdahl may have been a deserter but that he may have been an active collaborator with the enemy.

The Pentagon official added pointedly that no relevant congressional committee has sought access to the classified file, but that if such a request were made, key committee chairs would, under previous precedent, likely be granted access to it. Separately, the Pentagon confirmed Monday that it is looking into claims Americans died during the search for Bergdahl.

The administration announced over the weekend that Bergdahl's release had been secured, in exchange for five Taliban prisoners at Guantanamo Bay. President Obama was joined by the soldier's parents in making a public statement on the release Saturday evening from the Rose Garden.

Sources told Fox News that many officials in the Executive Branch are "quite baffled" by the White House's decision to allow the president to stand alongside Bergdahl's father this past weekend, given the father's history of controversial statements, emails and online posts.

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Asked Monday about reports that Bergdahl's father was communicating on Twitter with a man described as a Taliban spokesman, White House Press Secretary Jay Carney declined to comment on those reports but defended the administration's handling of the release.

"The fact is they are the parents of Sergeant Bergdahl. Their son was held in captivity for five years," he said. "And it was absolutely the right thing to do, for the commander in chief, for this administration to take action to secure his release, the last prisoner of war from the Afghanistan and Iraq wars."

Asked whether Obama stands by National Security Adviser Susan Rice's claim Sunday that Bergdahl served with "distinction," Carney said the president "stands by actions that he took as commander in chief" to secure his release.

Another administration official, whose duties are focused on counterterrorism, told Fox News when asked about the status of any investigations into Bergdahl's initial disappearance and his conduct over the last five years: "Everybody's looking at this. He's not going to get a free pass" in the interrogations that Bergdahl will face during his repatriation process. "He's going to have a lot of questions to answer -- a lot. Is he a hero? No."

Although this source had not seen the classified file described by the Pentagon source, the counterterrorism official agreed that given the high priority attached to the Bergdahl case over the last five years, the need for clarity about Bergdahl's actions before and during his time with the Taliban "would have been a high priority for intelligence tasking."

Asked if the process of repatriation would include questioning of Bergdahl geared towards determining whether he engaged in any forms of collaboration with the enemy, the counterterrorism official replied: "Of course. ... It's there. This is extremely untidy."

Officials noted that there were more than 50 cases in the Korean War where U.S. service personnel categorized as POWs were investigated for possibly having collaborated with North Koreans or the Chinese during that conflict.