He added that reports suggesting two Sierra Leone squash players had also gone missing were being treated as speculative at this stage.
The Indian Commonwealth Games Federation has been told to send both athletes home on the first available flight.
Following the addition of the three more medals, Team Nigeria now has four gold, five silver and two bronze medals.
A former Commonwealth Games athlete has been charged with assaulting two teenagers, allegedly throwing a glass into an 18-year-old man's face and punching a woman on a Gold Coast dance floor.
Two of the athletes failed to show up to compete in their events.
Martin said cleaners had found a needle in a cup in the apartment assigned to Babu and Thodi on Thursday.
Illegal immigration is a highly contentious political issue in Australia and Peter Dutton, the country's Home Affairs Minister, issued a warning to athletes in January that they would be deported if they overstayed.
"These athletes. were part of a team that had a training camp before getting to Gold Coast", he said in a statement.
"I think it's disappointing that athletes that have come didn't compete as they were scheduled to compete", he said.
"But these athletes are guests here in Australia, they are still within their visas and they have the right to travel freely", Grevemberg said.
But Mr Sharpe revealed there had been no positive tests so far at the Gold Coast Games.
"When the Commonwealth Games Federation says no tolerance, the Commonwealth Games Federation means no tolerance", Ms Martin said.
"There are mechanisms in place and they haven't breached their visas".