Fairfax and News Ltd reported a urine sample submitted by the 44-year-old South African in Brisbane last Tuesday under WBA regulations showed he had the banned stimulant Phentermine in his system.
The test, which has been forwarded to the WBA's global headquarters in Panama, was also said to have detected traces of Benzodiazepine, a valium-like product.
Williams defeated Botha in a unanimous points decision in Brisbane, but the fight ended after 10 rounds, instead of 12 as per WBA rules and as had been advertised.
Bookmakers refunded bets on Williams's controversial win and 44-year-old Botha challenged the rugby star to a rematch.
Williams, who was on the receiving end of some heavy blows from Botha in the final round, tweeted on Saturday that both camps knew it was a 10-round affair.
It's understood Botha's management bizarrely failed to tell the 44-year-old it had been cut to 10 rounds.
The ringside judges gave the Kiwi the victory 97-91, 98-94 and 97-91 which was greeted by considerable booing from the crowd.
Williams is set to lace up his boots for a NRL campaign with the Sydney Roosters.