Midland business leader Peter Suddock, chief executive of Dudley Zoo for more than 20 years, has been suspended on full pay pending an internal inquiry.
Mystery surrounds the reasons for Mr Suddock's absence from the zoo, where he has been chief executive since 1993.
It is understood his partner Jill Hitchman, who has worked as the zoo's head of media and communications, is no longer working in that role.
Mr Suddock, 68, is understood to be on gardening leave while an internal investigation is carried out.
A statement from Dudley Zoo said: "Peter Suddock, the CEO of Dudley Zoo, has been suspended on full pay pending an investigation into his conduct of certain affairs of the zoo.
"The suspension does not constitute disciplinary action by the zoo. Whether or not disciplinary action is taken will depend upon the outcome of the investigation."
Dudley councillor and former council leader David Sparkes, who sits on the zoo's board of trustees, said: "There is only one shareholder in the company that is Dudley Zoo and Castle and that is Dudley Council.
"I have kept that shareholder, in the form of the leader of the council, and the chief legal officer, informed of the situation."
Dudley Council has a long-term lease on the freehold of the zoo site.
Mr Suddock's career began in the engineering industry before he became chief executive of registered charity Dudley Zoological Gardens in 1993. He is also a former chairman of the Royal Wolverhampton NHS Trust.
Highly connected in the tourism sector, Mr Suddock has been chairman of the Heart of England Attractions Group, a consortium of West Midlands leisure attractions.
In an interview with the Guardian in 2007, Mr Suddock said of the time he took over as zoo chief executive in 1993: "It was crap. Crap. It was on the point of closure."
In 2000, the magazine Holiday Which? voted it Britain's worst zoo and Mr Suddock told the newspaper at the time: "The vast majority of the population in this part of the world can't afford to go to Asia, Africa, South America for holidays – they might do one, if they're bloody lucky, but not all three.
"So we've got to show them what wonderful species the world holds, and reinforce the message that we mustn't exploit them."
In its last available accounts for 2013, parent group Dudley and West Midlands Zoological Society Ltd said: "In 2013 we exceeded budgeted visitor figures and achieved a dramatic increase on the previous year.
"We welcomed 264,029 total visitors in the year, compared to 225,429 in 2012. This was an increase of 17 per cent, which is considerable growth. The society achieved a surplus after depreciation of £468,267."
Neither Mr Suddock nor Ms Hitchman could be contacted for comment.
Zoo Trust chairman Neil Cutler said: "I have no comment to make."