Nye was handling charges against Assange of sexual assault on two women.
This is a set back to the case against the online activist who is also being pursued by the United States for charges of espionage, thanks to his WikiLeaks project.
The Australian is currently holed up in the Ecuadorian embassy to London as he fights deportation to Sweden to face the charges.
Earlier in the month one of the alleged rape victims fired her lawyer Claes Borgstrom and accused him of hogging the media limelight rather than attending to the case.
Borgstrom is however not new to controversy. The lawyer, who has handled previous high profile cases, has been referred to by a high profile Swedish commentator as performing “the worst defence counsel job in modern Swedish history".
The happenings also precede a keynote lecture on the “Assange affair” to be delivered by a Swedish judge next Wednesday at the University of Adelaide to the displeasure of Assange who has termed the talk as outrageous.
"This development is part of a pattern in which senior Swedish figures, including the Swedish Foreign Minister, the Prime Minister and Minister for Justice, have all publicly attacked me or WikiLeaks," Assange said.
This is a view shared by Greg Barns, a barrister and spokesman for the Australian lawyer alliance.
"That a Swedish supreme court judge thinks this is acceptable tends to confirm the fears people have about the impartiality and robustness of the Swedish judicial system. It gives great currency to the belief that Mr. Assange's case in Sweden has been heavily politicised.”
It is however not clear whether the changes in the prosecution team and the plaintiff’s representation will have a major effect on the case.
Assange is a man portrayed by some as criminal and others as a human rights activist.
He is currently in with the chance of winning Human Rights Personality of the Year after failing to capture the Nobel peace prize in 2011.