The call from the WMA, which claims to represent physicians from 114 member countries, follows the Court of Arbitration for Sport (CAS) ruling in favour of the IAAF in its landmark legal case against South African double Olympic champion Caster Semenya.
Semenya, a two-time Olympic and triple world champion over 800m, had been hoping to overcome the regulations, due to come into effect on Wednesday (May 8).
WMA President Leonid Eidelman warned the organisation had "strong reservations about the ethical validity" of the IAAF rules, which could have a considerable impact on sport and International Federations.
Eidelman criticised the IAAF, claiming its regulations were based on "weak evidence from a single study, which is being widely debated by the scientific community" and said they should be immediately removed.
"They are also contrary to a number of key WMA ethical statements and declarations, and as such we are calling for their immediate withdrawal," Eidelman said.
The WMA had previously expressed its opposition to medically prescribing treatment to lower testosterone if the condition was not recognised as pathological.