EVERETT — The commanding officer of Naval Station Everett has been reassigned while the military investigates an allegation of sexual assault, the Navy said Monday.

James Duke Jr., 48, of Lake Stevens, faces a criminal court-martial hearing, which is similar to a civilian grand jury proceeding, according to a Navy news release.

Through his attorney on Monday, Duke said he is innocent and the “target of a malicious and false allegation.”

The allegation initially was reported to the Lake Stevens Police Department in January.

Duke’s girlfriend at the time told police that he sexually assaulted her after she turned down his request for sex, Lake Stevens police Cmdr. Dennis Taylor said.

Lake Stevens police worked closely with military investigators on the case, Taylor said. Duke declined to be interviewed by detectives. The Lake Stevens case was forwarded to Snohomish County prosecutors, who notified police in June they weren’t going to file charges.

Duke’s attorney said that the allegation was retaliation for him ending the long-term relationship.

“I am confident he will be cleared of this ugly and false accusation,” said Everett lawyer Anna Goykhman.

Duke had assumed command at Naval Station Everett at a ceremony on July 2, 2013. In July of this year, he was involved in an unrelated domestic disturbance near Lake Stevens. The Snohomish County Sheriff’s Office investigated but did not find evidence that a crime had occurred.

That disturbance involved an argument over a paternity test and child support, police records show.

Duke’s administrative reassignment is not an indication of guilt, according to the Navy news release.

Cmdr. Jeff Caulk, the executive officer of Naval Station Everett, has temporarily assumed the duties of commanding officer.

Before taking command in Everett, Duke was special assistant for Navy aircraft carrier reactors operations. During his Navy career, Duke commanded the USS O’Kane and served as reactor officer aboard the USS Abraham Lincoln. He has no criminal history, according to police reports.

Snohomish County’s second-largest employer, the Everett base is home to six ships and two Coast Guard vessels.

Reporter Gale Fiege contributed to this story. Rikki King: 425-339-3449; rking@heraldnet.com.