Defense minister Waldir Pires was to be replaced by Nelson Jobim, 61, a former justice minister, Supreme Court justice and lawmaker, a presidential spokesman said.
Pires was fired as Brazilian authorities faced sharp criticism over problems plaguing the aviation sector, after a TAM airlines Airbus 320 slid off a wet runway on landing at busy Congonhas airport on July 17.
The jetliner slammed into a building and burst into flames, killing some 200 people. Lawmakers said the jetliner's speed on impact was 175 kilometers per hour (109 miles per hour). It had slowed from 220-240 kph (137-149 mph) on touchdown.
Since the tragedy, all flights at Congonhas, the country's busiest hub, have been diverted to a secondary runway, which is closed in rainy weather.
The military runs Brazil's air traffic control system, and controllers have gone on strike periodically since Brazil's previous most-deadly air tragedy in September, when a GOL airliner collided with a small, private plane over the Amazon jungle.
The private plane's occupants were unharmed but all 154 persons aboard the jetliner were killed, prompting air traffic controllers to demand that Pires provide better working conditions and systems upgrades.
Pilots have long complained that the runway at Congonhas is slippery, especially in wet conditions, and several hundred meters (yards) shorter than a comparable one at New York's LaGuardia airport.
The runway was undergoing maintenance at the time of the Airbus crash and was newly resurfaced, but rain grooves had not yet been cut into the new surface.
After the crash, Lula insisted that the country's air safety did meet international standards, but yielded to political pressure calling for accountability for the disaster, whose after-effects lingered one week later in Brazil's aviation system.
Cascading delays continue throughout the country: 26 percent of all flights reported delays of more than one hour, while 12.9 percent were canceled, according to Brazilian airport authority Infraero.
To stem the congestion, Brazil on Tuesday stopped airline ticket sales from Congonhas airport, whose secondary runway was closed for rain late Tuesday and early Wednesday causing 70 percent of flights to be cancelled.
Rain also closed down three other airports in the country on Wednesday, TAM said.
Brazil's Gol airline asked its clients to postpone their travel if possible to July 30, and announced it will completely reorganize its flight schedule as of Monday.
Brazil's air force has offered planes to commercial airlines to help alleviate pressure on the country's chaotic air traffic network, as they did in December.
"When we see that the airlines do not have the means to provide for their passengers, we will take action," said Milton Zuanazzi, head of the civil aviation agency.
While authorities said international flights remain largely unaffected, some experts disagreed, noting that the disruptions could affect the entire region since Brazil serves as a vital bridge for flights headed to Europe and the United States.
Meanwhile, dozens of victims' relatives demanded quicker identification of the bodies.
Since the crash, 68 of the 187 Airbus passengers have been identified.
They included 90 from Porto Alegre in southern Brazil, where relatives gathered at Salgado Filho airport carrying photographs of their relatives killed in the crash.
Sao Paulo Justice Secretary Luiz Antonio Marrey justified the delay: "The bodies are badly burned, making identification difficult."
Officials said temperatures aboard the burning jetliner reached 1,000 degrees Celsius (1,800 degrees Fahrenheit) -- almost the temperature of a crematorium -- rendering the human remains almost unidentifiable.