ASOIF's statement is the latest shot across the US's bows regarding the case of 23 Chinese swimmers who were cleared to compete at the Tokyo Olympics in 2021 despite testing positive for a banned drug.
WADA received a clean bill of health over the matter in an interim report by retired Swiss prosecutor Eric Cottier on Tuesday.
Cottier said WADA had not mishandled the case though this failed to silence arch critic Travis Tygart, head of the US Anti Doping Agency (USADA).
WADA received unqualified support from the International Olympic Committee on Thursday and ASOIF made no bones about their disquiet with USADA and the American justice system on Friday.
Brent Nowicki, World Aquatics chief executive, has been subpoenaed to testify as part of the US criminal investigation into the affair.
The investigation was opened by the courts and the FBI, under the Rodchenkov Anti-Doping Act, at the request of a committee of the House of Representatives.
"The US criminal investigation into an anti-doping case on foreign soil, and the recent position of the US Anti-Doping Agency, threaten to undermine the role and independence of WADA, and by extension, trust and confidence in the global anti-doping system and the autonomy of sporting rules and regulations," read the ASOIF statement.
'Urgent clarification'
ASOIF raised a concern about whether athletes and others associated with sports could feel secure in travelling in the US which is "one of the largest sports markets in the world" and will host the 2028 Los Angeles Olympics.
"The US' extraterritorial investigation raises doubts about the personal safety of athletes, sport officials and representatives of international sport organisations and the confidence with which they may travel to the US for international sporting competitions and commitments," said ASOIF.
Indeed they suggested such uncertainties could prove costly to the United States.
"The investigation may lead IFs (International Federations) to consider the risks of allocating future international events to the US," read the statement.
"On behalf of its member IFs, ASOIF seeks urgent clarification from the US Olympic and Paralympic Committee and the Los Angeles 2028 Organising Committee for the Olympic and Paralympic Games regarding the position of WADA as an institution and respect for the fundamental principles of the World Anti-Doping Code."
The crisis arose when in April when the New York Times and German broadcaster ARD reported the swimmers had tested positive for trimetazidine (TMZ), a banned heart medicine which can enhance performance, at a domestic competition in late 2020 and early 2021.
It was determined by Chinese anti-doping authorities they ingested the substance unwittingly from tainted food at their hotel and no action against them was warranted.
WADA accepted the argument of the Chinese authorities and did not sanction the swimmers.
Some of them went on to compete in the Tokyo Olympics in 2021. Zhang Yufei won two golds and Wang Shun was also crowned Olympic champion.
Eleven of the swimmers have been selected for the Paris Olympics which start in a fortnight.
The case caused a global uproar, with US anti-doping authorities accusing WADA of a cover-up.
As a result, WADA set up an independent investigation overseen by Cottier.
"There is nothing in the file -- which is complete -- to suggest that WADA showed favouritism or deference, or in any way favoured the 23 swimmers who tested positive for TMZ," Cottier said in his report.
