This story was originally published April 1 at 11:03 a.m. and has been updated.

The Navy’s top officer is withdrawing the nomination of Rear Adm. Elizabeth Train to take over as director of naval intelligence and replace the three-star who has been hamstrung for more than two years by a lack of access to secret information.   Vice Adm. Ted Branch, who has been stymied for years in his job as the Navy’s top intelligence officer after his security clearance was suspendedrevoked in late 2013. 

The Navy's top officer is withdrawing the nomination of Rear Adm. Elizabeth Train to succeed Vice Adm. Ted Branch, who has been stymied for years in his job as the Navy's top intelligence officer after his security clearance was revoked in .

The withdrawal of Train’s nomination continues the dysfunctionuncertainty at the Navy’s top intelligence post that has dragged on for nearly 30 months. Vice Adm. Ted Branch’s security clearance was suspended after it came to light that he was under investigation for ties to the disgraced Malaysian contractor Leonard "Fat Leonard" Francis, who is at the center of the largest Navy corruption probe in decades.

Navy Times broke the news that Train, who leads is the commander of the Office of Naval Intelligence, was to be nominated to replace Branch almost 16 months ago, but since then the nomination has stalled. 

Vice Adm. Jan Tighe, commander of the Navy's Cyber Command, will be the Navy's pick to replace Branch and her nomination is working its way through the system, according to a Navy official who spoke on background. Her name has not yet been forwarded to the U.S. Senate for confirmation. Indeed, it took 10 months from when Train's name was first mentioned as Branch's replacement to when the service sent it to the Senate for confirmation.

Adm. John Richardson, chief of naval operations, thanked the career naval intelligence officer for her service but said the Navy was going in another direction.

"Rear Adm. Train has given 33 years of incredible service to our Navy and nation," Richardson said in a statement. "In recognition of her talents Admiral Train was nominated to be our next deputy CNO for Information Warfare (N2/N6).

"As the scope of the rapidly-changing information warfare environment has grown, I decided to go in a different direction. Liz Train is a valued and important member of our intelligence and information warfare leadership team and has performed superbly in her current assignment. I am grateful for her many years of service and the role she played in helping to keep America safe."

A Navy official who spoke on background said Train is set to retire after her change of command next week. Replacing Train as ONI bosscommander will be Rear Adm. Robert Sharp, who heads the intelligence office at U.S. Special Operations Command.

Francis, known in Navy circles as "Fat Leonard," pleaded guilty in January to charges of bribery, conspiracy to commit bribery and conspiracy to defraud the United States. As the head of husbanding firm Glenn Defense Marine Asia, Francis is accused of leading at least a decade-long scheme to overbill the Navy for ships pulling into ports across the Pacific, plying senior officers with wine, ship models, prostitutes, parties and golf to deepen his ties to Navy leaders in the region. to senior officers in the region and ship commanding officers who were passing through.

Branch has been stuck with less access to secret information than the lowliest ensign for more than two years, and his deputies have had to represent him in all classified meetings. Some have worried that naval intelligence has suffered without a three-star to attend top meetings.

Branch is under suspicion for ties to Leonard receiving a gift from Leonard during his time as CO of the carrier Nimitz in 2005. While he has not commented on the allegation, he has called the idea that he threatened national security "insulting."

"The shortest version of the story is, it's frustrating in the extreme," Branch said, according to a February story on Military.com. "Probably the most important point is, I am not a danger to national security, nor have I ever been, nor will I ever be, and the idea that I would be is insulting."