Napolitano defended the Obama administration's budget request for the FFDO program, which allows members of flight crews who have been approved by the Transportation Security Administration to be armed with guns during flights.
"As you all know, we're working under severe budget constraints," she said to Cravaack. "The FFDO program, as compared to the air marshal program, is not a risk-based program. So that's why that decision was made."
Cravaack argued that the House "recently passed a homeland security appropriations bill that would increase the FFDO funding."
But he said the budget proposals from the Obama administration "basically cut the program in half, would in essence eliminate it.
"If the funding level stands, will this administration work to clear the backlog -- and I'm saying the increased funding -- increase the backlog of pilots that are waiting to join the program," he asked Napolitano.
Napolitano responded that she does not make guesses about future decisions that may be made by the Homeland Security department.
"I don't speculate, I don't play 'what ifs,' " she said. "We'll see what happens."
Pressed further by Cravaack, Napolitano said: "If there is funding for the program, we will carry out the program."
Wednesday's hearing was not the first time the freshman Minnesota lawmaker and the homeland security secretary had a run-in over flight deck officers.
At a hearing in February, Cravaack asked Napolitano if flight deck officers were the "last line of defense for our traveling public."
“I think the armed cockpit door actually is," Napolitano responded then.
Cravaack referenced the February back-and-forth Wednesday, telling Napolitano "[L]ast time we had a little exchange regarding FFDOs, and I said the last line of defense was the FFDO."
Cravaack asked Napolitano if she wanted to "comment any further on that position."
"Well, I think FFDOs play a valuable part in airline security, aircraft security, which … involves multiple layers," she said. "I think in that exchange we talked about the FFDO, we talked about the cockpit door."