Nine bodies are thought to be trapped in the vessel
It hopes to recover the bodies of nine Japanese students and teachers believed to be trapped inside.
The 190-foot (38-metre) trawler, used to teach Japanese high-school students about the fisheries industry, sank off the Hawaiian island of Oahu when the USS Greeneville surfaced beneath it during an emergency drill.
The commander of the submarine was reprimanded at a final hearing into the accident and forced to retire.
Click here for diagram of operation
The Ehime Maru is 610 metres (2,000 feet) below the surface.
The wreckage was harnessed to a giant lifting frame suspended beneath an oil-rigger, called Rockwater 2. Once it reaches shallower waters, remotely-operated vehicles will inspect the vessel and monitor the lifting.
The Navy expects it will take divers about 33 days to completely search the ship for remains.
The Navy said last week that the trawler, from Uwajima, southern Japan, was not as badly damaged as first feared. It has spent $60m so far on trying to recover the victims.
There was a public outcry in Japan over the accident. Those killed were two teachers, four 17-year-old students, and three crewmen. Twenty-six people survived.
Hawaii has often been a choice spot for training voyages, as it is considered a safe destination with its calm waters and medical facilities.
In April, US Navy Commander Scott Waddle, 41, was found guilty of dereliction of duty and reprimanded for his role in the accident.
Related to this story:
US to search sunken Japanese trawler
(06 Aug 01 | Americas)
Top-level inquiry into trawler sinking
(18 Feb 01 | Asia-Pacific)
US finds sunken Japanese trawler
(17 Feb 01 | Asia-Pacific)
Sub tragedy leaves Japanese town bitter
(16 Feb 01 | Asia-Pacific)
Sub tragedy: How drill turned to disaster
(16 Feb 01 | Asia-Pacific)
Civilian: I was at crash sub's controls
(15 Feb 01 | Asia-Pacific)
Civilian was at US sub controls
(14 Feb 01 | Asia-Pacific)
Relatives visit sub collision site
(13 Feb 01 | Asia-Pacific)
Sub victims 'to be compensated'
(12 Feb 01 | Americas)
Sub collision prompts review
(16 Feb 01 | Asia-Pacific)