Australian Olympic swim team Cameron McEvoy, Eamon Sullivan, James Roberts, James Magnussen, Matt Targett and Tommaso D'Orsogna.
On Monday, the board of Swimming Australia reportedly told Mr Nugent at a meeting that his services are no longer needed, following the disastrous performance of the country's swimming group in 2012's London Olympics. The board apparently made the decision Thursday last week.
The board however denied the decision.
"Leigh actually approached us to discuss his future and where he would best fit into the new structure of the high performance unit," Barclay Nettlefold, president of Swimming Australia, said in a statement on Wednesday.
"In those discussions it soon became very clear that while he still wanted to remain involved in the sport, he didn't want to continue in the position of head coach."
Mr Nugent became the group's head coach in 2009. But his post got enmeshed in serious jeopardy following the London Olympics when the Australian swimming team failed miserably due to lack of discipline and behavioural problems.
In two separate reviews, it was found that Mr Nugent ignored complaints when members of Australia's men's 4x100 relay team harassed the female swimmers at the Games. The men's group, according to swimmers James Magnussen and Eamon Sullivan, took Stilnox in the lead-up to the Games, despite the ban placed by the Australia Olympic Committee.
The reviews also highlighted a poor swimming leadership culture and management.
"If these sorts of things have occurred we will certainly make sure that the Integrity Panel looks into these areas," Mr Nettlefold had said in February.
"Leigh will have to put his case to it, I would have thought ... whilst we are fully supporting Leigh and understand the pressure he was under - he was frazzled by it all."
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