According to the Washington Post, the three men are also being investigated for allegedly breaking curfew during Trump's stop in Vietnam.
They have reportedly been reassigned from their jobs at the White House following the incident, which is said to have happened in Vietnam.
Another similar incident took place in August during Vice President Mike Pence's visit in Panama where military personnel violated the same curfew rule and brought unregistered women to their hotel rooms, The Hill reported.
The Secret Service directed media inquiries to the WHCA.
Military Staff Removed From White House After 'Incident' On Trump's Asia Trip
Laura Seal, a Pentagon spokeswoman, confirmed the investigation. Those service members were flown home before Mr. Pence arrived.
The agency's role is to prevent eavesdropping on presidential communications and to ensure that White House officials can be securely reached worldwide at a moment's notice.
The White House Communications Agency comprises former service members who provide "vital information services and communications support to the president and his staff". While the specifics of their conduct was not yet known, the service members could lose their security clearances and face other disciplinary measures if found guilty.
The WHCA, which is part of the White House Military Office, employs about 1,200 staffers from all branches of the military and are assigned to duties on four-year tours.