Bousquet was the first man to break 21 seconds for the 50m freestyle
World swimming governing body Fina has approved a number of hi-tech racing suits that had initially been rejected for July's world championships in Rome.
Among those passed are the X-Glide and Jaked 01, used by Alain Bernard and Frederic Bousquet respectively in setting world records.
However, Bernard's 100m freestyle time of 46.94 was not approved by Fina.
Bousquet's 50m freestyle time of 20.94, also set at the French championships in April, is still pending approval.
Fina said Bernard's was not approved as a record because the suit was unacceptable at the time.
"This decision will have serious consequences for swimming and us swimmers," Bernard said in a statement. "Fina's positions are contradictory and impossible to understand."
The French Federation said it would appeal the decision.
"This is pitiful. This is not the end of the story. We must now defend our athletes' best interests," French Federation technical director Christian Donze said.
Bernard's coach Denis Auguin added: "These are inconsistent decisions once again. Some times set with some swimsuits are approved while others set with equivalent suits are not."
The world record remains in the hands of Australian Eamon Sullivan in 47.05.
After more than 100 world records were broken in 18 months, Fina decided to review 348 suits from 21 manufacturers.
A panel sent back 136 to manufacturers, which could then modify their designs.
However, the Jaked 01 which was re-submitted without having any modifications, was approved, while the X-Glide, after slight changes to reduce the amount of polyurethane used, was also given the green light.
The emergence of some swimsuits in recent years had caused controversy because some experts, including some top swimmers, believe their use gives an unfair advantage in the pool.
Critics of the all-polyurethane suits claim the compression and buoyancy which results from their use, called 'air-trapping', helps boost speed. The old suits only had polyurethane plates.
Fina had already stipulated swimsuits should not cover the neck and must not extend past the shoulders and ankles, and limited the thickness and buoyancy of the suits.
The decision to approve the Jaked suit will delight the Italian hosts of the world swimming championships as their team is sponsored by Jaked, an Italian company.