New Zealander David Howman, who leaves his post after a 13-year tenure as WADA director-general on Tuesday, said any other option would have put clean athletes in jeopardy.
"Every lab accredited has to acquire a quality of level of standard so they don't deliver false positives or, worse, false negatives. Our expert group says this lab must be suspended until those are remedied.
"When you host an event like this, you've got to send samples to a [nearby] laboratory. It doesn't necessarily have to be on site. Regrettably this one also had to send samples out of town during the 2014 [FIFA] World Cup.
"I'm sure the IOC will have a Plan B because there are plenty of accredited labs on this [American] continent and plenty in Europe. They'll need to work out what to do and will no doubt be talking to us in the meantime."
The Rio lab was readmitted in May 2015 after the credentials were revoked two years earlier and remedial work was required. At the time WADA president Craig Reedie said, "My people believe that they [the laboratory experts] are capable of doing the job... it is absolutely essential [an accredited lab is there] to proper conduct of an Olympic Games".
In 2015 WADA found Rio had the capacity to undertake at least 3000 tests at the Olympics. Around 5000 tests were carried out at the 2012 London Games.
"They'll be looking to put the foot on the accelerator," Howman said. "I'm not in a position to say how long that will be, but our expert scientists made the decision because the quality was not up to standard and we'd hate to see mistakes made during the Games.
"We are simply doing our job, and will continue to do so."