The 27-year-old could need surgery after hurting his pectoral muscle followed by two to three months out.
Williams injured his shoulder and chest while playing for Japanese Top League club Panasonic Wild Knights at the weekend and was rushed to hospital for an MRI scan.
New Zealand's heavyweight boxing champion initially said on his Twitter page "results nothing serious, small tear so hopefully still be able to (box)".
Arriving in Sydney on Tuesday, however, Williams said the muscle needed more tests, the results of which could force the November 24 fight with Botha in Brisbane to be called off.
"At the moment it is a little bit in doubt," he said at Sydney airport before beginning his preparations to face the 44-year-old Botha.
"I just came back here straight away," Williams added. "I've got to get some scans and see how the pec is, see the extent of the injury."
Nine News reported that the hulking centre had undergone tests and faced surgery after being spotted at the headquarters of National Rugby League side the Sydney Roosters.
Williams, who began his career in rugby league, had been expected to quit union to join the Roosters.
He the world champion All Blacks and Waikato Chiefs for a lucrative 12-match deal in Japan worth an estimated £62,000 a game.
Williams smashed his shoulder into the turf after a flying tackle in Panasonic's 23-20 win over Kintetsu Liners on Saturday and left the ground with his arm in a sling.
The injury could bring a premature end to his Japanese season, with Panasonic having seen little return halfway through their investment.
Interim NRL chief executive Shane Mattiske has warned Williams that his return would only be sanctioned once the necessary documentation had been signed.
Williams said in June that he would honour a handshake agreement with Roosters supremo Nick Politis but to date, no contract has been put forward to the NRL.
If serious, the player's injury further complicates the situation for one of New Zealand's biggest sporting names.
"The Roosters understand that if they are to bring Sonny Bill to the game, they need to approach us about that," Mattiske said.
"They need to get to a point where they've got a contract they can bring to us for registration. At this stage we're waiting for that to happen."
- Sports & Recreation