The legendary promoter has also stressed he worries about the mental wellbeing of the unbeaten Brit, who was due to defend his title against Demetrius Andrade on October 20.
Saunders, 29, was denied a boxing license by the Massachusetts State Athletic Commission yesterday, for failing an out-of-competition doping test in August.
Namibian knockout artist Walter Kautondokwa has stepped in at late notice for the southpaw, with the vacant title on the line in Chicago.
Speaking in a statement, Warren said: "Boxing is a dangerous sport and the 100 per cent health – both physical and mental – is paramount at all times.
"Because of the mental anguish brought about by this case and out of respect for the WBO, Billy Joe will with a heavy heart relinquish his world title, whilst this issue is in the process of being resolved.
"Legal proceedings will then be issued against the MSAC following the Supreme Court hearing.
"The MSAC in their refusal to grant a licence to Billy Joe have benefited his scheduled opponent, Andrade, who hails from nearby Rhode Island and who will now fight for a vacant title against the next ranked Namibian Walter Kautondokwa."
While he also said: "This year Billy-Joe has had 4 tests carried out by UK Anti-Doping (UKAD) and a subsequent test performed by VADA has contained no traces of any prohibited stimulants.
"This is not some technical legal argument. It is the simple facts and the truth. The MSAC, in their decision to deny a licence to Billy-Joe, have wilfully refused to properly apply the code of WADA to their ruling.
"Further the MSAC refused to properly consider submissions from Billy-Joe’s representative despite him being present at the hearing.
"Cases such as these can take a considerable time to be heard and adjudicated on and, given the damaging effect these accusations of wrongdoing have had on the mental wellbeing of Billy Joe, he is in no position to continue in his profession until such a time as his name has been cleared."
Saunders will likely miss out on a £1.7million pay day in Boston, in what comes as another setback for the 2008 Olympian.
He was fined £100,000 last month after a video emerged of him offering a woman £150 worth of drugs in exchange for a sex act.
And he once again hit the headlines for the wrong reasons after rapping out prostitutes just says after the footage went viral.
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