But investigators tell ABCNEWS he also stopped verbally calling out targets even though he was reportedly tracking the Japanese boat on the surface.
When the USS Greeneville rose to periscope depth, investigators now believe the Ehime Maru was only about a mile away, directly behind the submarine. The captain and officer of the deck both looked in that direction through the periscope, but did not see it.
The Navy said the $900 million submarine may be more seriously damaged than first thought.
Sources say the rudder post may need replacement, which would require forging an entire new piece to keep the sub running quietly.
The court of inquiry, convened for March 5, will determine whether disciplinary action should be taken against any or all of the officers named as subjects, and could ultimately lead to a court martial. Under Navy rules, the presiding officers at a court of inquiry can name additional subjects or "parties" at any time during the proceedings.
As the investigation moves forward, the Coast Guard continues to search for the nine missing at the request of the Japanese government.
A search which has so far covered more than 30,000 square miles — an area roughly the size of Maine — at a cost of more than $1 million.
"We are going to continue to search as if they're still out there," Greg Fondran, spokesman for the U.S. Coast Guard.
The National Transportation Safety Board left Hawaii today having reached no conclusions on its investigation.
Waddle, who could face court-martial proceedings, along with other top submarine officers after a weeks-long investigation by the Navy, said he would not speak to investigators with the NTSB until after the Navy investigation is completed.
Political Implications for U.S.-Japan Relations
The sinking of the fishing vessel has further strained relations between Washington and Tokyo, and comes after a top U.S. military officer in Okinawa was forced to apologize for calling local politicians “nuts” and “wimps” in a private e-mail.
U.S. military personnel have been implicated in a series of crimes, ranging from sexual harassment of a schoolgirl to arson accusations.
The incident has also caused the popularity of the government of Prime Minister Yoshiro Mori to further plummet, with the Japanese media now speculating on not whether but when the premier will resign.
On Monday, Mori told a stunned Diet that he didn’t know the phone number to the crisis management center in his own residence, and was unable to get updates on the tragedy days after it happened.
ABCNEWS' Neal Karlinsky and NewsOne contributed to this report.