Police Service of Northern Ireland (PSNI) Deputy Chief Constable Mark Hamilton is to retire later in 2024, with recruitment for a replacement to begin immediately.
The Policing Board said his departure, after 30 years in policing, was “in line with contractual entitlements”.
Mr Hamilton has been absent from work since a medical procedure a year ago.
He became second-in-command in 2020.
Mr Hamilton was caught up in the same controversy which caused Simon Byrne’s resignation as chief constable in September 2023.
Both men were criticised following a Belfast High Court ruling which found two junior officers were unlawfully disciplined over an arrest made at a Troubles memorial event.
At the time the Police Federation, which represents rank and file officers, passed a vote of no confidence in Mr Hamilton and others.
Earlier in 2024, Mr Hamilton appeared set for secondment to the Department of Justice, but the move never happened.
In a statement, the board thanked him for “his distinguished service to the community”.
“Board members are assured the retirement is in line with contractual entitlements, and that there is no disparity between our approach to this retirement and that taken in relation to other officers who have retired from the service, regardless of rank,” the statement said.
“The board respects the confidentiality of personal information in relation to the DCC, as it does with all of its employees.”
In October, Chief Constable Jon Boutcher made Chris Todd his temporary deputy in Mr Hamilton’s continuing absence.
The PSNI added it would be advertising on Thursday for a permanent replacement to Mr Hamilton.
The PSNI’s latest accounts show his salary to have been about £200,000.