Games officials said race walker Irfan Kolothum Thodi and triple jumper Rakesh Babu were found to have a syringe in their room in the athletes' village on the Gold Coast.
The disappearance comes just hours after Home Affairs Minister Peter Dutton warned that athletes who breach their visa conditions would be tracked down, locked up and deported.
One who failed to appear was Ulrich Rodrigue Yombo who skipped Wednesday morning's weigh-in for his quarter-final bout in the 81kg division against Canada's Harley O'Reilly.
"The team was here in Warwick training, but the reality is we are three hours away from the Gold Coast, it is quite a trip", Cr Dobie told news.com.au.
Most athletes and officials are on visas that remain valid until May 15 but Dutton was concerned by instances in which athletes missed their events at the Games "when that was the reason they were here".
The first three left on April 8, before two more followed the next day.
"Why did they take action on both athletes?"
It came as Grevemberg said Cameroon officials have pleaded for Gold Coast residents, tourists and athletes to come forward with any information regarding the Cameroon athletes that left the village earlier this week.
"We have no idea which direction they headed in", Mr Molombe said.
Cameroon officials on Wednesday made a decision to fly 14 athletes, including the entire 12-man basketball team, home immediately after they had completed their competitions.
During the London 2012 Olympics, 21 athletes and delegates either vanished or asked for asylum in the UK.
The athletes' visas are yet to expire, with authorities aware of the incident but not now pursuing a missing person's case. "They are still within their visas, they have the right to travel freely", Commonwealth Games Federation chief executive David Grevemberg said.
It's obviously disappointing that I think some of the athletes that have come didn't compete as they were scheduled to compete.