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Botha - a former heavyweight champion who claimed he did not know his bout with Williams was set for 10 rounds - tested positive for phentermine in his system.
The 44-year-old submitted a urine sample on Tuesday last week, the Sydney Morning Herald said, and the test revealed the presence of phentermine, a banned stimulant.
It also showed traces of benzodiazepine, a valium-type product. The drug test had been forwarded to the WBA's headquarters in Panama.
Australian National Boxing Federation committee member John Hogg cast doubts on the report, telling Australia's News Limited there were no compulsory drug tests required for boxers in Queensland.
He had never heard of the Australian Sports Anti-Doping team spot-testing fighters in the state.
"I would think I would have heard about ASADA testing Botha or Sonny Bill because they have never showed up to boxing gyms in Queensland or on fight night," Hogg told News Limited.
Witnesses who saw Botha in his dressing room before the fight told the Sydney Morning Herald he was relaxed and lying on the floor as Williams entered the ring first.
But when the fight got under way, he was alert and taunted Williams, while trying to put him off his game with a series of late shots.
Williams' manager Khoder Nasser told Firstline he wasn't surprised with the alleged revelation.
"I wasn't really surprised, because I couldn't believe someone had the fitness like that. He was still going after getting punched and bruised so badly and he was still standing."
A leading sports doctor told the Sydney Morning Herald that phentermine and benzodiazepine has opposing effects.
"One puts you to sleep, one keeps you awake. Phentermine is part of the go-fast group, as I call them, which is similar category to all of the adrenalin amphetamines ... anything that is a stimulant that keeps you awake and improves your reflexes."
Before the drugs revelation, Nasser said Williams was flattered by an approach from David Tua's camp - but a rematch with Botha may be a more realistic prospect.
Williams tweeted he was willing to get back in the ring with the South African boxer.
"After, God willing, having a good footy season Ill gladly rematch Mr Botha. Even in South Africa," Williams wrote on Twitter.
Williams' win over Botha in Brisbane was tarnished by allegations of poor sportsmanship amid confusion surrounding the length of the bout.
Nasser said both camps knew the fight was intended for 10 rounds, though that was contradicted by Williams in the build-up to the bout.
"I think his last four or five fights went the distance,'' Williams said on Thursday. "He'll do 12 rounds pretty easy.''
That was reinforced at the pre-fight weigh-in where the boxers' introduction was prefaced by the announcement the fight was set for "12 times three-minute rounds''.
But Nasser insisted that Boxing Queensland dictated the bout was set for 10 rounds. He said Botha knew this and his protestations were for the promotion of the fight and possible rematch.
"The commission has said that both managers agreed it was 10 rounds before the fight,'' Nasser said.
"Francois Botha's an A-class promoter and I commend him. I think he was great in every sense, and he was even greater after the fight.
"He might be able to talk himself into a rematch. Though the fight was totally one-sided, he's been doing a remarkable job.''
Yesterday, Williams wrote on Twitter that Boxing Queensland had acknowledged to both parties the fight was supposed to be 10 rounds. He also said he had received a congratulatory phone call from the World Boxing Association.
Another possibility - albeit an unlikely one - is for Williams to defend his New Zealand heavyweight championship title against Tua.
Tua's promoter, David Higgins of Duco, told the Herald on Sunday Williams should accept to restore credibility to the tarnished sport.
Even an ageing Tua would prove a fierce challenge for the former All Black.
Williams will have to wait until the conclusion of his commitments with the Sydney Roosters, with the NRL season taking priority until September.
Whether Williams will be allowed to fight again in Brisbane remains to be seen. Boxing Queensland would not return calls but an unnamed official told the Sunday Mail that crisis talks would be held to curtail Nasser's future promotions.
- APNZ with nzherald.co.nz