The sailors' relatives, US military officials and some 300 crew members of the guided-missile warship will join the private event.
The service will be held on Tuesday at the naval base in Yokosuka, southwest of Tokyo, where the badly damaged destroyer USS Fitzgerald is based, a navy spokeswoman said.
The sailors' relatives, US military officials and some 300 crew members of the guided-missile warship will join the private event, she added, without releasing other details.
The memorial comes as investigators probe what happened in the early hours of June 17 when the ship collided with the Philippine-flagged ACX Crystal in a busy channel near the destroyer's home base, a gateway to container ports in Tokyo and nearby Yokohama.
There have been around 30 ship collisions over the past decade in the area, including a 2013 incident in which six Japanese crew died, according to the Japan Coast Guard.
The US sailors, aged 19 to 37, were found by divers in flooded sleeping berths a day after the collision tore a huge gash in the side of the Fitzgerald.
Japanese investigators have interviewed the Filipino crew of the 222-metre (730-foot) cargo ship, while the US authorities are also probing the deadly crash.
Rear Admiral Brian Fort has been appointed to lead the US investigation, the navy said in a statement dated Thursday.
The much-larger cargo ship's crew -- who were not injured -- apparently took nearly an hour to report the collision.
Japan's coastguard initially said the crash happened at 2:20 am Saturday (1720 GMT Friday) based on when it was reported by the Crystal's crew.
But they later told Japanese investigators the incident actually happened almost an hour earlier at 1:30 am.
Authorities are also investigating why the cargo ship made a sudden turn at about 1.30 am, and a sharp turn after it reported the accident around 2:20 am.