The agency had delayed hundreds of flights last week in response to being forced to operate with about a 10 percent reduction in the number of people monitoring flights.
Obama's comments Tuesday echoed concerns raised last week by the group that lobbies for airports, the Airports Council International-North America (ACI-NA).
The ACI-NA said last Friday that it was happy to see the furloughs and flight delays end, but worried about the impact of shifting the money that had been earmarked for airport improvements.
"Airports Council International – North America is relieved that air traffic controller furloughs will soon end, returning our nation’s air transportation system to full capacity," ACI-NA Board Chairman David Edwards Jr. said in a statement after the final passage of the FAA bill.
"The travel and financial impacts over the last week for passengers, airlines, and airports were substantial, and if such impacts continued there would have been a devastating negative economic effect on our nation," Edwards continued. "However, we are very disappointed that the Airport Improvement Program (AIP) was used to pay for this fix, as these funds were paid by passengers to maintain and enhance airport runways and taxiways, not fund FAA operations.”
Obama said he agreed to the short-term FAA bill because "the alternative, of course, is either to go ahead and impose a whole bunch of delays on passengers now, which also does not fix the problem."
He added that Congress was not likely to agree to a broader sequester bill if he turned down the FAA measure.
"Frankly, I don't think that if I were to veto, for example, this FAA bill, that that somehow would lead to the broader fix," Obama said. "It just means that there'd be pain now -- which they would try to blame on me -- as opposed to paying five years from now. But either way, the problem's not getting fixed."
Still, Obama said that he wished Congress had taken another course in response to the flight delays.
"If in fact they are seriously concerned about passenger convenience and safety, then they shouldn't just be thinking about tomorrow or next week or the week after that, they should be thinking about what's going to be happening five years from now, 10 years from now or 15 years from now," Obama said. "The only way to do that is for them to engage with me on coming up with a broader deal."
The Airports Council agreed with Obama's sentiments.
"ACI-NA supported other common sense bipartisan legislation that did not use AIP to eliminate the furloughs," it said. "Airports agree that passenger delays and inconvenience cannot continue, but raiding capital funding to pay for FAA operations is unprecedented and does not take into account the need to make critical safety, security and capacity improvements."
The ACI-NA said it was not giving up on pushing Congress to fund airport improvements, however.
“ACI-NA will continue to work with Congress to obtain critical infrastructure funding to ensure airports can meet passenger safety and security needs as well as continue to generate jobs and economic development in hundreds of communities throughout the United States,” Edwards said.
Obama also said Tuesday that it was important to fund airport improvements, citing a recent study of airports that found Cincinnati International Airport was the only U.S. airport in the top 30 facilities in the world.
"Not one U.S. airport was considered by the experts and consumers who use these airports to be in the top 25 in the world," Obama said. "What does that say about our long-term competitiveness and future?
"And so when folks say, 'Well, there was some money in the FAA to deal with these furloughs,' well, yeah, the money is this pool of funds that are supposed to try to upgrade our airports so we don't rank in the, you know, bottom of industrialized countries when it comes to our infrastructure," Obama continued. "We're using our seed corn short term."
-This post was updated with new information at 1:16 p.m.