After the discoveries, the government ordered stepped-up searches on the more than 7,000 aircraft in the nation's commercial fleet as a precaution.
Still, officials said they did not believe the bags were placed there as a prelude to a terrorist attack.
"It doesn't appear to be a terrorist event," FBI Director Robert Mueller said during a visit to the FBI field office in Houston. "I think it is safe to fly."
Sources tell CBS News' Bob Orr the FBI has identified a suspect in the case. One investigator says "it looks like an inside job."
Homeland Security Department spokesman Brian Roehrkasse described the searches as "a precautionary measure." They were expected to be completed within a day without disrupting service.
Southwest employees doing routine maintenance found the items in small plastic bags left in the lavatories of planes in New Orleans and Houston on Thursday night, according to a statement from the airline. The items were turned over to government officials and the FBI and Transportation Security Administration immediately began investigating.
The statement said the items appeared "intended to simulate a threat" and that each bag was accompanied by a note that "indicated the items were intended to challenge Transportation Security Administration checkpoint security procedures."
"We will not speculate on who might have left these items on board," the statement said.
Southwest said security checks of its entire fleet of 385 aircraft found no other suspicious items.
All airlines conduct routine searches of their planes. Roehrkasse said a government directive that went out after the bags were found instructed airlines "to make sure the searches are done in a comprehensive and thorough manner."
The New Orleans flight had originated in Orlando, Fla., and was scheduled to go on to San Diego later Thursday night, said Southwest spokeswoman Beth Harbin. The crew reported a lavatory wasn't working and a maintenance worker discovered the bag at about 9 p.m., she said. The other aircraft was in Houston for routine maintenance when the bag was discovered a short time later.
In addition to the box cutters and notes, the bags contained bleach, matches and modeling clay, according to a senior law enforcement official speaking on condition of anonymity. The clay was formed to mimic a plastic explosive, while the bleach could have been used to demonstrate how a dangerous liquid could be smuggled aboard an aircraft. It could also be thrown in a person's eyes to temporarily blind them.
The notes also included the exact date and location the items were placed on board the planes, the official said. But the official would not provide other details, other than to say the items found on the New Orleans plane were not placed aboard in Orlando, according to one note.
The 19 al Qaeda operatives who hijacked planes and crashed them on Sept. 11, 2001, used box cutters as weapons. After the attacks, box cutters were added to the list of items banned from carryon bags.
Government officials played down the possibility of a terrorist connection, though FBI spokeswoman Susan Whitson said members of the bureau's joint terrorism task forces are involved in the investigation.
Harbin said Southwest does not believe the items found were connected to a plot to hijack the airplanes.
Al Qaeda and its affiliated terrorist groups have long had an interest in using aircraft as weapons. The FBI and Homeland Security Department have issued numerous warnings about possible tactics terrorists could use, including use of small carryon items such as cameras to blow up airplanes.