The Los Angeles Times reports ( http://lat.ms/142Q0YF) Malibu Capt. Joseph Stephen had denied wrongdoing before Tuesday's announcement.
Assistant Sheriff James Hellmold says Stephen had decided to retire but had yet to go through the process, so he was relieved of duty.
Retired Chief Ronnie Williams and Capt. Anthony Ward are also being investigated following a deputy's allegations.
Stephen told the Times the deputy's allegations are untrue but declined to say whether they had a sexual relationship. Stephen says he was never her direct supervisor.
Williams, who retired four years ago, told the Times she was never assigned to his division, so he doesn't understand how he could have coerced her to do anything.
Information from: Los Angeles Times, http://www.latimes.com