One of the umbrella groups, representing 150 European brands, has decided to inspect factories for safety flaws already checked by members of the second group.
Brad Loewen, chief safety inspector for the Accord group, which includes H&M and Tesco, said he would push ahead with the fresh inspections, saying he had some "concerns" with ones already undertaken.
"We just want to be sure," Loewen told AFP.
The second group called Alliance, representing mostly US retailers such as Walmart and Gap, branded the reinspection move a "setback for garment factory safety efforts in Bangladesh".
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The groups were set up after the collapse of the Rana Plaza building that revealed woeful conditions for the sector's three million workers who stitch clothes for Western brands for poor pay.
The garment factory complex collapsed last April killing more than 1,100 workers in one of the world's worst industrial disasters.
Western retailers came under intense pressure to compensate the victims and clean up the $22 billion sector, the mainstay of impoverished Bangladesh's economy.
The decision to reinspect has enraged Bangladesh's garment manufacturers, who have already shut down 21 factories that the groups have deemed unsafe, retrenching tens of thousands of workers.
"It also created confusion as to which inspection report a factory must follow."
Head of Alliance, Ellen Tauscher, defended its own inspections of 600 factories, saying its experts had used safety and fire standards agreed by both groups.
But Loewen said he had "concerns" about inspections carried out by individual retailers who are members of Alliance, without elaborating on what the concerns were.
He said he did not have a problem with inspections conducted by experts on behalf of Alliance itself.