Air Force Gen. Ramon Cardoso said that the Mistral, a French Navy amphibious assaut ship hunting for remains of the airliner, has spotted an undetermined number of bodies in the ocean, but has not year reached them.
"We have received information that bodies have been spotted by a French ship but we will only be able to confirm how many, once they are retrieved from the ocean," he said.
Brazilian search planes have struggled with poor visibility, but "search efforts will continue in those regions where low altitude overflights are possible," Cardoso told a news conference.
"It is becoming more and more difficult to find and recover bodies," he said. "And the chances of recovering the bodies of all the passengers of the Air France flight are very remote."
Wednesday was the first day since Saturday that no bodies were recovered. Forty-one have been retrieved from the sea so far.
Cardoso said Brazilian officials would meet next week to decide whether to call off search efforts on June 19 or extend them until June 25. Ocean currents have scattered remnants of the plane over a vast stretch of water from off the shores of Africa to seas near South America.
So far, investigators have focused on the possibility that external speed monitors - Pitot tubes - iced over and gave false readings to the plane's computers.
The plane's manufacturer Airbus encountered new problems Thursday when an A330-220 carrying 203 people made an emergency landing in Guam after an electrical fault sparked a small cockpit fire, Jetstar airline reported.
Company spokesman Simon Westaway said a pilot put out the fire with an extinguisher and no one was injured.
Airbus, meanwhile, said it sent an advisory to airlines June 8 analyzing the automatic messages transmitted by the doomed Air France jet. Airbus spokesman Stefan Schaffrath said one of the messages showed a change of cabin pressure equal to an altitude change of more than 1,800 feet (548 meters) per minute. Schaffrath said Airbus does not yet have enough information to interpret that fact.
Air France received replacement Pitot tubes for the model of jet that crashed arrived just three days before the fatal accident, airline chief executive Pierre-Henri Gourgeon told journalists on Thursday.
Air France ordered the replacements on April 27 after pilots noted a loss of airspeed data in flight on some Airbus A330 and A340 models, he said.
The incidents were "not catastrophic" and planes with the old Pitots are considered airworthy, Gourgeon said.
"Because I am not convinced that the sensors are the cause of the accident, and we have said it, I had no need to issue a press release the day after the accident," Gourgeon added, responding to criticism that there was a lack of transparency.
"It's perhaps because we spend too much time with the families and not enough the press that you say this," he told an association of aerospace journalists in Paris.
In London, Tom Enders, president and chief executive of Airbus, told reporters that suggestions in France's Le Figaro daily that its A330 and A340 aircraft would be grounded was irresponsible. He said it is not Airbus' decision whether to ground planes, but that of the regulatory authorities.'
Enders warned against "premature speculation" about the cause of the crash and said investigations can often take months. The head of an association that groups 36,000 European pilots, Martin Chalk, defended the Airbus models, which make hundreds of flights a day.
The Flight 447 crash and the Jetstar emergency "are completely unconnected," said Chalk, president of the Brussels-based European Cockpit Association. "There is no threat to safety."
French and U.S. officials have said there were no signs of terrorism, and Brazil's defense minister said the possibility wasn't considered. But France says it has not been ruled out.
Air France hopes that the plane's flight recorders will be recovered, but even without them, examinations of the debris and bodies recovered from the crash are expected to shed new light on what happened to the plane, he said.
"We will know much more, I think, after the autopsies allow us to better understand the technical causes of death and when the debris have been examined by experts," Gourgeon said. "In a week there will be a little more information but the important point will be the recorders."
The French nuclear submarine Emeraude, hunting the data and voice recorders of the jetliner, cruised deep in the ocean to try to detect their signal pings.
Finding the boxes in the deep waters presents a formidable task, given the possibility that they could have come to rest amid jagged underwater mountains and that their signals will start to fade in about three weeks.
The submarine's crew plans to check 13 square miles (35 square kilometers) of ocean bottom a day, using sonar to try to pick up the boxes' acoustic beacons.
The United States has sent two underwater audio devices capable of picking up signals even at a depth of 20,000 feet (6,100 meters).
A Dutch search ship chartered by French investigators loaded one device Wednesday in the northern port of Natal and was expected to reach the search area by Sunday. A second Dutch ship was scheduled to pick up the second device this weekend.
Each device will be towed slowly in a grid pattern while 10-person teams watch for signals, U.S. Air Force Col. Willie Berges said.
If a box is located, the Emeraude will launch the remote-controlled mini-sub Nautile, which had a key role in the search for the wreckage of the Titanic, to recover it.
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Marco Sibaja reported from Recife and Emma Vandore from Paris. Associated Press writers Greg Keller in Paris, Stan Lehman in Rio de Janeiro and Slobodan Lekic in Brussels contributed to this report.
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