Toronto, Canada – Thompson took leave from his job in December after a claim of "inappropriate behavior" against him was reported to Swimming Australia by an anonymous source through local media.
The claim is under investigation.
"The acceptance of the redundancy is not related to the independent investigation being conducted by Louise Donohoe SC," a representative of Thompson said in a statement.
"Swimming is a sport that prides itself on professionalism, hard work and success, and to continue to maintain and develop those values at all levels, we believe this new structure is the best way forward," SA CEO Kevin Neil told the statement.
(Reporting by Ian Ransom; Editing by Alastair Himmer)