Saugy's lab is responsible for testing samples during next year's soccer World Cup in Brazil after the Rio lab was stripped of its WADA licence to test for banned substances last year.
The scientist, however, said building a lab from scratch capable of processing the thousands of tests conducted during Olympic Games in time for the 2016 Olympics would be a "tremendous task", even with more than two years to go.
"This is a big challenge. It means now the laboratory has been revoked and, to our knowledge, they are rebuilding a new building for the laboratory of the Olympics in Rio, and they have to rebuild the entire team," he told Reuters Television.
"Of course the Summer Olympics, with 12,000 athletes, have many, many more samples than you have at (the) Sochi (Winter Olympics) or during the World Cup, for example," Saugy said.
The World Anti-Doping Agency ruled in August that the Rio laboratory did not meet the International Standard for Laboratories (ISL) and revoked its WADA accreditation.
Samples taken at the World Cup will now be flown across the Atlantic to Switzerland, raising doubts that positive tests from players will be discovered before their next matches at the tournament.
"In that case it will be huge testing because all the players from all the teams will be tested pre-competition," Saugy said.
"So it will be quite a lot, 32 teams and certainly more than 20 samples per team. So in less than one month it will be a huge work to be very rapid, so we will certainly invite other people from other laboratories to our laboratory in order to be fast and to work 24 hours a day."
But the challenge of completing a new laboratory for the Olympics is even harder.
"It's a tremendous task, I think, for the Brazilian authorities now to rebuild this, something credible, something which is working perfectly and you can believe it, and we are discussing that point.
"The IOC (International Olympic Committee) is thinking a lot about that. WADA is also organising discussions in order to solve a problem because we know that beginning from scratch, two years is very, very short and they are almost beginning from scratch for the Olympics in 2016."
Rio Olympics organisers are already struggling with their preparations and IOC President Thomas Bach travelled to Brazil last month to identify problems and improve cooperation between the government and local organisers.
He has warned Rio there was "no time to lose" as the Brazilian metropolis prepares for the first Olympics on the South American continent.
- Summer Olympics
- Sports & Recreation
- 2016 Olympics