The agency's director said that helping expose drug cheats came with personal risks for those who go public.
WADA and the International Olympic Committee (IOC) are under pressure to stamp down on drug cheats with Russia in particular in the spotlight for what WADA calls state-sponsored doping across multiple sports over several years.
WADA Director General Olivier Niggli said whistleblowers such as the Russian athlete Yuliya Stepanova and her husband Vitaly -- who fled to the United States because of fear of reprisals -- were invaluable sources of information to help bust the drug cheats.
But he said others contemplating following their lead needed to know they would be safe.
"Anti-doping agencies can only do so much in the fight against doping," the Swiss lawyer Niggli, who replaced the long-serving David Howman in July last year, told journalists after appearing on a panel at the Tackling Doping in Sports conference in London.
"We desperately need whistleblowers. But to encourage their cooperation and so on we can only do so much.
"We need law enforcement on our side to help provide protection to the whistleblowers and they are the only ones who can do it."
Niggli said that helping expose the drug cheats came with personal risks for those who go public.
"I would think in most cases before a whistleblower becomes exposed you would have secured necessary protection with relevant law enforcement in the particular jurisdiction," he said.
"That should be the right process going forward."
The Stepanovs are the most high-profile to come forward, playing a major part in blowing open doping across Russian sports.
Vitaly, who worked for the discredited Russian Anti-Doping Agency (RUSADA), and his runner wife fled Russia fearing for their safety following their revelations in 2014 about widespread doping in the country.
Russian President Vladimir Putin referred to her as "Judas" but the Russian track and field team was barred from last year's Rio Olympics and there was a total ban on Russians at the Paralympics.
"The Stepanovs was the first case of its kind and was done differently in that it was exposed by the media first," said Niggli, warning those contemplating following their example should avoid going to the press with their revelations as it blows their cover instantly and puts them in danger.
"The recent Russian whistleblower decided to do it on TV," said Niggli, referring to the runner Andrey Dmitriev, who spoke to German media.
"It was his call and we were not interfering with that. We will take the information but after that he is not of any use as no one is talking to him anymore in Russia.
"Once he is out there it is unlikely he will get anymore information.
"We would certainly not encourage them going public until everything is secured because once they are out there it is far harder to protect them."