The deputy, who has not been identified, was not assigned to supervise the cadets, according to the department. No further information into the allegations was released.
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The department is also launching a review of the explorer program, but said it is not aware of any other misconduct allegations.
Sheriff Jim McDonnell ordered "swift and appropriate action" be taken to hold anyone accountable who is not protecting the cadets and the department program.
He added that all department members need to "hold themselves to the highest ethical and moral standards at all times."
The explorer program is one of the department's top initiatives.
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The announcement comes amid a probe of the Los Angeles Police Department's cadet program, which has resulted in arrests over stolen patrol cars and equipment as well as an officer-cadet sexual relationship.
A group of protesters called for an independent review of the LAPD's cadet program Tuesday afternoon.
"Stop the cadet program. LAPD must defund the cadet program and publicly acknowledge and take ownership of its history," said Nia-Amina Minor, with Black Lives Matter.
The LAPD said calls for the end of the program are "misguided and misinformed" and would prevent "educational and skill-building opportunities for thousands of young adults."