Captain Abdel-Salam al-Mahdawi was taken by a unknown suspects late on Wednesday night, officials said.
"He was taken by force under the threat of weapons from a location close to the criminal investigation police offices," said one police official who declined to be named, because he was not authorized to speak to the media.
Benghazi, cradle of the armed uprising which saw the end of Muammar Gadhafi's rule in Libya, has been plagued by poor security and assassinations of police and military by militias.
A body charred by hydrochloric acid was found in the city's Buhmeida district, Benghazi police chief Mustafa al-Regayig told state radio. It has not been identified yet, he said.
"We can't confirm or deny that the body is of Captain al-Mahdawi at this time," he said.
Police officials told Reuters Mahdawi had been ready to name suspects over the murder of a former Benghazi police chief.
Faraj al-Deirsy was shot to death in front of his home in November, police and interior ministry sources said at the time.
The US ambassador to Libya and three other Americans were killed in an attack on the US consulate in Benghazi in September.
Police investigators and legal experts have avoided taking on that case because they say they have not been guaranteed protection from groups they believe carried out the attack.
BENGHAZI, Libya (Reuters) -- The head of Benghazi's criminal investigation police unit is missing after he was seized by armed men, police officials said on Thursday.