"It's literally crawling at the bottom of the ocean so it's going to take a long, long time," Houston said.
The locator beacons on the black boxes have a battery life of only about a month and Tuesday marked exactly one month since the plane vanished. Once the beacons blink off, locating the black boxes in such deep water would be an immensely difficult, if not impossible, task.
"There have been no further contacts with any transmission and we need to continue (searching) for several days right up to the point at which there's absolutely no doubt that the batteries will have expired," Houston said.
If, by that point, the U.S. Navy towed pinger locator has failed to pick up more signals, the sub will be deployed. If it maps out a debris field on the ocean floor, the sonar system on board will be replaced with a camera unit to photograph any wreckage.
Earlier, Australia's acting prime minister, Warren Truss, had said the Bluefin 21 autonomous sub would be launched on Tuesday, but a spokesman for Truss said later the conflicting information was a misunderstanding, and Truss acknowledged the sub was not being used immediately.
Houston earlier said the two sounds heard Saturday and Sunday are consistent with the pings from an aircraft's black boxes.
Defense Minister David Johnston called the sounds the most positive lead and said it was being pursued vigorously. Still, officials warned it could take days to determine whether the sounds were connected to the plane that vanished March 8 on a flight from Kuala Lumpur, Malaysia, to Beijing with 239 on board.
"This is an herculean task it's over a very, very wide area, the water is extremely deep," Johnston said. "We have at least several days of intense action ahead of us."
Houston also warned of past false leads such as ships detecting their own signals. Because of that, other ships are being kept away, so as not to add unwanted noise.
"We're very hopeful we will find further evidence that will confirm the aircraft is in that location," Houston said. "There's still a little bit of doubt there, but I'm a lot more optimistic than I was one week ago."
Such optimism was overshadowed by anguish at a hotel in Beijing where around 300 relatives of the flight's passengers most of whom were Chinese wait for information about the plane's fate.
One family lit candles on a heart-shaped cake to mark what would have been the 21st birthday of passenger Feng Dong, who had been working in construction in Singapore for the past year and was flying home to China via Kuala Lumpur. Feng's mother wept as she blew out the candles.
A family member of another passenger said staying together allowed the relatives to support one another through the ordeal. "If we go back to our homes now it will be extremely painful," said Steve Wang. "We have to face a bigger pain of facing uncertainty, the unknown future. This is the most difficult to cope with."
Investigators have not found any explanation yet for why the plane lost communications and veered far off its Beijing-bound course, so the black boxes containing the flight data and cockpit voice recorders are key to learning what went wrong.
"Everyone's anxious about the life of the batteries on the black box flight recorders," said Truss, who is acting prime minister while Tony Abbott is overseas. "Sometimes they go on for many, many weeks longer than they're mandated to operate for we hope that'll be the case in this instance. But clearly there is an aura of urgency about the investigation."
The first sound picked up by the equipment on board the Ocean Shield lasted two hours and 20 minutes before it was lost, Houston said. The ship then turned around and picked up a signal again this time recording two distinct "pinger returns" that lasted 13 minutes. That would be consistent with transmissions from both the flight data recorder and the cockpit voice recorder.
The black boxes normally emit a frequency of 37.5 kilohertz, and the signals picked up by the Ocean Shield were both 33.3 kilohertz, U.S. Navy Capt. Mark Matthews said.
Houston said the frequency heard was considered "quite credible" by the manufacturer, and noted that the frequency from the Air France jet that crashed several years ago was 34 kilohertz. The age of the batteries and the water pressure in the deep ocean can affect the transmission level, he said.
The Ocean Shield is dragging a pinger locator at a depth of 3 kilometers (1.9 miles). It is designed to detect signals at a range of 1.8 kilometers (1.12 miles), meaning it would need to be almost on top of the recorders to detect them if they were on the ocean floor, which is about 4.5 kilometers (2.8 miles) deep.
The surface search for any plane debris also continued Tuesday. Up to 14 planes and as many ships were focusing on a single search area covering 77, 580 square kilometers (29,954 square miles) of ocean, said the Joint Agency Coordination Center, which is overseeing the operation.
Associated Press writers Kristen Gelineau in Sydney, Rod McGuirk in Canberra, Australia, and video journalists Isolda Morillo and Peng Peng in Beijing contributed to this report.