Ocean Shield has detected four signals linked to aircraft black boxes, helping to narrow down the vast search zone. But the last confirmed ping came on Tuesday last week and officials suspect the batteries are now dead.
The retired air chief marshal stressed the enormous difficulties in working at great depths in such a remote location.
"This is an area that is new to man," Houston said, expecting to find a lot of silt. "It's not sharply mountainous or anything, it's more flat and almost rolling, but we understand... that part of the India Ocean has a lot of silt on the bottom.
"And if we have silt on the bottom, that can be quite layered, quite deep and that will complicate how things are on the bottom. It's around 4,500 meters."
The Bluefin-21 is equipped with side-scanning sonar and will initially focus on 40 square kilometers (15 square miles) of seabed in the vicinity of the detected signals.
But Houston explained that the US-made vessel operates slowly, with each mission taking a minimum of 24 hours to complete.
The device needs two hours to reach the bottom, where it will work for 16 hours producing a high-resolution 3-D map before surfacing in another two hours.
Downloading and analyzing data requires a further four hours.
But while the mini-sub could take the search a step closer towards visually identifying any wreckage, Houston repeated his longstanding note of caution that nothing was guaranteed.
He noted that after Air France Flight AF447 crashed in the Atlantic Ocean in June 2009, it took nearly two years to retrieve the black boxes from a depth of 3,900 meters.
"However, this is the best lead we have and it must be pursued vigorously. Again I emphasise that this will be a slow and painstaking process."
The Bluefin-21, a 4.93-meter long sonar device, weighs 750 kilograms and can operate down to 4,500 meters -- roughly the depth of the ocean floor where the pings were detected.
Houston also said the search for floating material from the plane would end in the coming days.