Eric Fanning (in civilian clothes) as Acting Secretary of the Air Force in 2013

[UPDATED with Army comment] WASHINGTON: Under pressure from Sen. John McCain, Acting Army Secretary Eric Fanning will step aside until the Senate confirms his nomination as secretary. The official reason is a 1998 statute about nominees not being allowed to do the job de facto before they’re legally confirmed for it. The real reasons, however, may be Guantanamo Bay and the famously combative senator.

According to a Pentagon statement this morning, unspecified “members of the Senate Armed Services Committee expressed some concerns about his [Fanning’s] designation as Acting Army Secretary pursuant to the Vacancies [Reform] Act.” Passed the last time a Democratic president was bitterly at odds with a Republican Congress over nominations (and everything else), the 1998 law says that “a person may not serve as an acting officer for an office under this section, if…. the President submits a nomination of such person to the Senate for appointment to such office.”

For legislative language, that seems pretty clear. But the Pentagon says Fanning’s role is “consistent” with the Act and he is merely stepping aside as a show of “comity.” [UPDATED: When I asked a Department spokesman to elaborate, Lt. Col. Joe Sowers told me only that “Mr. Fanning’s designation as Acting Secretary of the Army was consistent with longstanding Executive branch interpretation of the Federal Vacancies Reform Act.  Members of the Senate Armed Services Committee, however, expressed some concerns about that interpretation of the Act.  As a show of comity to address these concerns, Fanning has agreed to step out of his acting role to focus on achieving confirmation in the near future.”]

Anyway, haven’t we had officials serving as acting this or acting that while awaiting nomination in the past? “I am sure we have,” one Senate staffer told me, “but we haven’t always had John McCain as SASC chairman.”

John McCain

In other words, previous chairmen might have let a situation like Fanning’s slide despite the law — but McCain don’t play that game.

There are two factors raising the political stakes. One is that Fanning would be the first openly gay secretary of any military service — a milestone for Obama and a millstone for many Republicans. The other is that Kansas Senator Pat Roberts has placed a hold on Fanning’s nomination in protest against the administration possibly sending prisoners from Guantanamo Bay to the continental United States, potentially including sites in Kansas.

Holds are a routine delaying tactic in the modern Senate, however, and Roberts’ action in and of itself seems unlikely to have derailed the nomination. The Vacancies Reform Act issue, however, apparently was enough to force Fanning to step aside, if only for now.

“It’s an unusual situation to be sure,” one Democratic Hill staffer told me. “I would have thought the Administration would have gotten at least a tacit nod from McCain before they named him acting.” That said, the staffer continued, Fanning stepping aside in deference to SASC’s concerns is “not damaging as long as it helps him get confirmed.”

The Senate Armed Services Committee’s only official comment? “Senator McCain is looking to hold a hearing to consider Mr. Fanning’s nomination as soon as possible.”

How long will that take, though? The Pentagon statement pointedly complains that Fanning was nominated “well ahead of former Secretary McHugh‘s retirement in late October, [but] the U.S. Senate did not take up his nomination prior to McHugh’s departure.” Such delays, like holds, are again the norm in the modern Senate.