Speaking to Reuters during a WADA meeting in Lausanne, Switzerland, Tygart said as long as sports bodies were represented on WADA, the anti-doping organisation could not deliver on its promise to crack down on cheats.
"It is the fox guarding the hen house," Tygart told Reuters when asked whether WADA was independent. "Clearly not. No question about it."
WADA has been in the spotlight since 2015 over a Russian state-backed doping scandal that involved more than 1,000 athletes and led to the suspension of the country's athletics federation and its anti-doping agency.
Russia's track and field athletes were banned from last year's Rio de Janeiro Olympics but the International Olympic Committee refused to exclude its entire Olympic team, despite being urged to do so by WADA.
WADA's foundation board and executive committee are composed equally of representatives from the Olympic movement and governments.
"We have to get clear first what WADA's role is. It has to be that of a global regulator and then we can see what it costs to fund this," Tygart said.
He said money, a main concern for WADA, would be made available from the world of sport and its stakeholders like broadcasters and sponsors once their product was protected by an independent organisation.
Tygart, who was a strong supporter of a blanket ban on Russian athletes in Rio, said WADA should be able to hand out sanctions for non-compliance to countries or federations, something it cannot do at the moment.
He said in that way sport would be protecting its own product more effectively and fans would get exactly what was advertised.
His comments come three days after the United States Olympic Committee issued a position paper calling for an independent global anti-doping agency.
(Reporting by Karolos Grohmann; Editing by Mark Trevelyan)
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