Sources said Mugishaâ€™s resignation letter was approved by the Board of Trustees headed by John Nagenda last week, but awaits the approval of the tourism minister.
Mugisha said in an interview that he planned to take up a job with a global conservation NGO. He did not give details.
However, sources said Mugisha resigned because he was fed up with corruption and political interference in UWA and did not want to be compromised.
His four-year contract was to end in March next year.
Nagenda said they had accepted Mugishaâ€™s resignation and that he would be leaving UWA this May.
â€œWe have accepted his request with regret, but you canâ€™t stand in the way of someone who is trying to improve himself,â€ Nagenda said, adding that they had got several good people who could replace him.
Mugisha, who is a graduate of forestry of Makerere University, and of natural resources management of the University of Florida, USA, rose from the lower ranks to executive director, replacing Dr. Robbie Robinson, a South African expatriate who left three years ago.
UWA was formed a decade ago after the merger of the Uganda National Parks and the Game Parks.
Eric Edroma, a lecturer at Nkumba University, Moses Okuab and Dr. Yakobo Moyini also served as UWA chiefs in the late 1990s.
Sources said Nagenda and Mugisha have zealously blocked many people who wanted to grab resources meant to protect animals for personal interest.
Nagenda, who is also a presidential adviser on media affairs, has assisted in harnessing the UWAâ€™s potential, but denied reports that they had been fighting corrupt individuals within the tourism ministry.
â€œI know nothing about it. We would definitely fight it (corruption),â€ Nagenda said, adding that they would protect the interests of animals and the welfare of people.
Nagenda said the term of his board that was appointed by the Minister of Tourism two years ago expires this July. He said he was not sure it would be re-appointed.
Mugisha said he had introduced good systems to drive the UWA.
UWA boss quits over corruption