Barclay Nettlefold resigned on Sunday and is being investigated for allegedly making an inappropriate remark to a female team consultant and another allegation of misbehaviour.
"This is a difficult time for Swimming Australia and we recognise there are no easy solutions," the body's Chief Executive Mark Anderson said in a statement.
"Firstly, Barclay Nettlefold resigned ... Now a major sponsor has withdrawn its support from Swimming Australia. This is obviously disappointing but we respect the decision."
Traditional swimming powerhouse Australia slumped to their lowest Olympic medal haul in 20 years in London last year with a solitary gold medal and no individual titles.
Swimming Australia was also rocked by critical reviews into its governance and a scandal involving top swimmers taking the banned sedative Stilnox in a team bonding session in the leadup to the London Games.
The Australian Sports Commission cut funding to the country's elite swimming programme by 5.8 percent for the current financial year.
While Swimming Australia did not name the outgoing sponsor, local media reported it to be power company Energy Australia.
"The sport of swimming has been rebuilding since London. There is much to do," Anderson added.
"We have made a number of cultural and governance changes but the events of the last few days have crystallised the need for further endemic organisational and cultural change."
- Sports & Recreation
- Swimming & Diving
- Swimming Australia