Phelps and Schmitt issued their calls in written testimony released ahead of their appearances before a US Congressional oversight and investigations subcommittee hearing in Washington to be held later Tuesday.
Both Phelps and Schmitt, along with US Anti-Doping Agency (USADA) chief executive Travis Tygart, who is also due to testify at the hearing, took aim at WADA over the recent revelations concerning 23 Chinese swimmers who tested positive for banned prescription heart medication trimetazidine (TMZ) in early 2021.
None of the 23 swimmers were suspended or sanctioned after WADA accepted the explanation of Chinese authorities that the results were caused by food contamination at a hotel where they had stayed together.
In separate revelations published by the New York Times last week, it emerged that three of the swimmers -- including two 2021 Tokyo Olympic gold medallists and a current world record holder -- tested positive for banned substances several years earlier.
WADA has rejected charges from USADA that it engaged in a cover-up and China has denied any wrongdoing in the matter.
However Phelps and Schmitt hit out at WADA's handling of the case, saying trust in the body amongst athletes had been damaged by the scandal.
Phelps, 38, winner of a record 23 Olympic gold medals during five Olympic Games appearances, compared the current situation to 2017, when he last called for WADA reforms in a hearing before US lawmakers over the 2014 Russia doping scandal.
"It is clear to me that any attempts of reform at WADA have fallen short, and there are still deeply rooted systemic problems that prove detrimental to the integrity of international sports and athletes right to fair competition, time and time again," Phelps said in prepared testimony.
"I urge Congress to use its considerable leverage with WADA to make the organization independent and effective. It can't reasonably be a coincidence that WADA has yet again succumbed to the pressures of international sport to do the expedient at the expense of the athlete."
'Whispers' of China doping
Phelps said "close friends" had been potentially impacted by the decision to allow the Chinese swimmers who failed tests in 2021 to compete at the pandemic-delayed Tokyo Olympics.
"Many of them will live with the 'what ifs' for the rest of their lives," Phelps said. "As athletes, our faith can no longer be blindly placed in the World Anti-Doping Agency, an organization that continuously proves that it is either incapable or unwilling to enforce its policies consistently around the world."
Schmitt meanwhile was a member of the US 4x200m freestyle relay team that took silver in Tokyo behind China. That race was one of five events in which Chinese swimmers among the 23 who tested positive for TMZ won medals.
The 34-year-old said while she had heard "whispers of doping by the Chinese team" throughout her swimming career, she initially had no reason to doubt the legitimacy of China's 4x200m gold medal in Tokyo.
"We respected their performance and accepted our defeat," Schmitt said. "But now, learning that the Chinese relay consisted of athletes who had not served a suspension, I look back with doubt.
"I plead, on behalf of US athletes: hold WADA and the global anti-doping system accountable. If we win, let it be because we earned it. And if we lose, let it be because the competition was fair.
"We need the International Olympic Committee, NBC, sponsors, and fans to demand integrity in our sport."
Tygart meanwhile, a long-time critic of WADA, said in prepared testimony that failure to implement reform of the drugs watchdog would be "committing an unacceptable injustice to today’s athletes, fans, and sponsors who believe in and invest in fair and clean competition."
Tygart suggested that funding of WADA should be conditional on the agency setting up an "an independent expert committee" that makes the decision on all positive tests that do not result in an anti-doping rule violation and public announcement.
"The rules require this in all positive cases of this type and WADA has now finally admitted that China should have determined these 23 cases to be violations and therefore should have announced them back 2021," Tygart said.
