Congress refuses to gut the one program the Transportation Security Administration has offered to minimize: pilots who pack guns.

The House just passed an amendment in its Homeland Security appropriations bill that would boost funding for armed-pilot training by $10 million. That throws a sharp rebuke at both the TSA and the Obama administration, which proposed chopping financing in half.

The showdown exemplifies a larger tension over which programs created in the aftershock of Sept. 11 should endure — and what actually keeps Americans safe.

“The last line of defense is the pilot’s ability to defend the cockpit,” Rep. Chip Cravaack (R-Minn.), who was a gun-toting pilot when he served as a Federal Flight Deck Officer, told POLITICO. “There are always holes, even with the most scrutiny. This is a significant deterrent for terrorists.”

Cravaack’s amendment would pump the training program to $35.5 million by pulling funds from TSA screener payroll and maintenance accounts. Cravaack, vice chairman of the Transportation and Infrastructure Aviation Subcommittee, said current funding levels leave a backlog of eager participants waiting for background checks. The exact number of armed pilots remains classified, but it’s in the thousands.

The program grew out of legislation that created the TSA. The law passed with bipartisan support in 2002 and made it possible for pilots to volunteer for weeklong training and follow-ups on weapons handling. Pilots have never found reason to use their guns.

Cravaack and other proponents say the administration intends to dismantle the decadelong program through blistering cuts. Both TSA and the White House point to newer safety plans they see as a better use of money. The administration has recommended slashing the program from $25 million to $12.5 million and chopping $36.5 million from the Federal Air Marshal Service’s $929.6 million budget.

In its funding request, the Office of Management and Budget cited enhancements to aviation security, such as comprehensive screening and locked cockpit doors, that “have greatly lowered the chances of unauthorized cockpit access and represent a comprehensive and redundant risk-mitigation strategy that begins well before passengers board the aircraft.”

Kimberly Thompson, a spokeswoman for TSA’s Aviation Security Advisory Committee, said the agency supports multilevel security but must recognize financial realities. “As we continue to face declining budgets, we have to prioritize security investments based on risk,” she said. She highlighted the thousands of law enforcement officers and federal air marshals who take to the skies.

The program’s defense lingers partly on cost-effectiveness. The Air Line Pilots Association has calculated it costs $15 per flight for armed pilots compared with more than $3,000 for federal air marshals. That has to do with compensation. Pilots don’t get paid for their law enforcement propensities.

The crew has snagged some high-level backing. Transportation and Infrastructure Chairman John Mica (R-Fla.) applauded the recent House amendment, praising the TSA program even as he took a jab at the agency. “It would be foolish to gut security programs that actually work, like the Federal Flight Deck Officer program, in which our airline pilots bear much of the training costs and help ensure the cockpit is defended,” he said.

Sen. Barbara Boxer (D-Calif.), who helped craft the initial legislation, said she continues to support funding. Boxer asked for a $5 million boost to the program in a March letter to the Senate Homeland Security Appropriations Subcommittee. She described more than 700 professionals waiting to complete training. “It’s an effective program that trains pilots to serve as the last line of defense against attacks on passenger planes,” she told POLITICO in a statement.

The Senate Appropriations Committee has approved $24 million for the program, $1.46 million below last year. A committee report attributed the decrease to the “constrained budget environment” and chided the administration for deeper cuts. The report said the White House’s funding drop would “prevent thousands of dedicated flight crews who volunteer for this program from training that could protect commercial flights and the passengers on them.” The Senate has yet to take up the bill.

The notion of gun-toting pilots did not always receive such support.

The Air Transport Association of America, in conjunction with 21 airline CEOs, voiced its hesitation in a 2002 letter to Congress. They said the “idea of intentionally introducing thousands of deadly weapons into the system appears to be dangerously counterproductive.”

No one has suffered injuries from the weapons, but in 2008, a pilot’s gun went off and punctured a small hole in the plane.

A spokeswoman for the association, now known as Airlines for America, said it supports the program “as one part of the layered approach to security, including advanced intelligence, barriers and screening.”

As they battle against their first significant cuts, pilot-packing supporters counter safety concerns with reminders about the person behind the controls.

“The pilot has something far more dangerous when he flies — an aircraft full of jet fuel,” said Brian Darling, a former Senate staffer who helped write the legislation and now works for The Heritage Foundation. “They’re already flying a weapon of mass destruction.”