Sports scientist David Pease (40) last year turned down a job offer to work with elite athletes at the Australian Institute of Sport in Canberra to stay at the university's High Performance Centre.
But the uncertain future of the flume - the only one in the southern hemisphere and one of only six in the world - resulted in Mr Pease resigning from his role last week.
"If I knew the flume was staying I probably wouldn't have made the move," he said.
The University of Otago would not comment on Mr Pease's resignation when contacted yesterday.
"The future of the flume remains under review," School of Physical Education dean Prof Douglas Booth said.
Mr Pease accepted a deputy head role at the Australian institute's aquatic testing, training and research department.
He will work with elite Australian swimmers and triathletes as they aim for gold at Commonwealth and Olympic Games.
"Here, I am on my own, but in Australia I will be around other people interested in swimming," he said.
Mr Pease moved to Dunedin from Colorado, United States, after hearing a $2 million flume would be built at the university.
It was opened by Sir Peter Blake in April 1998.
A "who's who" of sportsmen and women have utilised the flume, including Phelps.
He visited the flume to test a suit for Speedo in 2003.
Speedo's latest suit, the LZR, was tested extensively in Dunedin before this year's Beijing Olympics.
The suit has since been credited with the record-breaking performances of many swimmers.
Mr Pease, the only specialist on the flume at the university, is concerned the 21m long flume would not be utilised - or sold - once he leaves to start his new position in September.
He said the flume was regarded as the best in the world and "in my opinion it should stay".
With no flume at the Australian Institute of Sport, Mr Pease sent a "cheeky email" to his new employers saying he knew where they could buy one.
"But I don't want it to go from here. It belongs here."
