In the letter, seen by the BBC, they say the Wada review “appears to be a ‘check the box’ exercise that will be substantially limited… and thus fail to reveal the whole truth.”
They added: “Once again, we are heading into another Olympic and Paralympic Games with serious concerns about whether the playing field is level and the competition fair.
“The decisions made by Wada, the way they were made, and the lack of transparency has undermined our confidence in Wada’s stated mission to ‘lead a collaborative worldwide movement for doping-free sport’.
“As athletes, we have to trust Wada to set and enforce standards that will ensure fair play and protect our rights. Wada’s failure to follow its own rules and procedures in the wake of the positive tests of these 23 Chinese athletes has broken this trust.
“Given this, we are asking you… to create and announce a truly independent investigation… perform an audit and ensure that Wada is held accountable to all stakeholders in the handling of this matter; and initiate an independent review that results in greater independence and oversight of Wada and its decisions so that Wada can fulfil the promise it makes to clean athletes and the integrity of the Olympic and Paralympic Games.
“…We believe this is the only way forward.”
Wada told the BBC that it “acted in good faith at all stages and in line with the policies and applicable rules.
“Mr Eric Cottier is entirely independent of Wada, the Sport Movement and Governments. He is a well respected prosecutor of 39 years’ experience.”
Gupta’s role is potentially important as governments fund half of Wada’s budget.
International Olympic Committee president Thomas Bach has said he has “full confidence” in Wada.
But Usada chief executive Travis Tygart said Wada and Chinada had “swept these positives under the carpet”.
Wada responded by saying those claims were “completely false and defamatory”, and had been referred to lawyers.
The Paris Olympics starts on 26 July.
Britain’s Olympic champion Adam Peaty and UK Anti-Doping have also called for greater transparency from Wada.
UK Sport chair Katherine Grainger told BBC Sport the issue was “incredibly unsettling for our athletes”, a “very disappointing moment for us all” and “should not be happening at this crucial time”.