Bluefin-21 is an almost 5m-long vehicle that can create a sonar map of the sea floor. On Monday officials said each mission was expected to last 24 hours, with 16 hours spent on the ocean floor, four hours' diving and resurfacing time, and four hours to download data.
The submersible has a safety feature that brings it to the surface if it exceeds its performance capabilities.
Australian officials have said previously that they are confident they are searching in the right area for the missing plane.
But ACM Houston warned on Monday that the search of the sea floor could be a long, painstaking process that might not yield results.
The sea where the Bluefin-21 is searching is estimated to be about 4,500m deep, but experts say there could be variations on the sea floor.
ACM Houston said on Monday that other, larger vehicles that could go deeper than the Bluefin-21 were being looked into, but it depended on "the outcome of what we find when we go down and take a look".
Officials have no idea yet why the plane diverted so far from its intended flight path. Investigators are looking at options including hijacking, mechanical failure, sabotage and pilot action.
Recovering the flight recorders is seen as key to understanding what happened to the plane.