The officer also allegedly previously told another man he was questioning that he would not be arrested if he stuck his head in a toilet, the document said.
Rabago, who remains on restricted duty, and Reginald Ramones, who left the department in August, were arrested and charged earlier this year with depriving a man of his civil rights.
Rabago has pleaded not guilty.
As part of a deal with prosecutors, Ramones on Wednesday pleaded guilty to a lesser charge that he knew Rabago committed a civil rights violation but did not report it.
The homeless man, identified in court documents only as the initials SI, “knelt down before the urinal and licked the urinal,” according to Ramones’ plea agreement.
Rabago then allegedly “laughed as he told other officers that SI had just licked the urinal,” it added.
Myles Breiner, representing SI, claimed there was physical force involved in getting him to lick the urinal during the January 2018 incident.
The lawyer said: “He submitted to the coercion and the duress of a bunch of officers who found it amusing to force him to place his face in a urinal.”
He added: “It makes no difference whether you’re a prince or a pauper, policeman, prosecutor or the president of the United States. Everyone is accountable and no one is above the law.”
Mr Breiner said his client is currently in prison for a parole violation in a drug case.
Ramones claimed in court that Rabago persuaded him not to tell authorities what happened in the public toilet and to delete their text messages about it.
Rabago told him to say he was joking when he talked about making the man lick the urinal, Ramones claimed.
Ramones repeatedly said both men were innocent during meetings with their lawyers and did not mention either bathroom incident, according to Rabago’s defence lawyer Megan Kau.
She added: “I think he got scared and he’s now saying things he wouldn’t necessarily have said before.”
Ramones faces up to three years in prison when he is sentenced in February.
Acting Honolulu Police chief Jonathon Grems, who is filling in for police chief Susan Ballard, said in a statement that the department was not aware of any earlier incidents involving Rabago.
He asked anyone with information to contact the police commission or the department’s professional standards office so an investigation can be opened.
Two other officers were also placed on restricted duty when Ms Ballard turned the case over to the FBI last year.
They have since returned to full duty, police spokeswoman Michelle Yu said, adding that an administrative investigation is ongoing.
Associated Press contributed to this report.
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