The National Beef Association said an unofficial ban, imposed in mid-July by buyers in the Netherlands and Belgium, "could be the end of the export industry".
For security reasons, the Worcestershire farm from which the infected calves originated has not been identified.
A Defra spokesman said that the unofficial boycott was unjustified.
NBA director Kim Haywood said the farmer who exported the infected calves cannot be held responsible, as there was a disease reservoir in the UK. She warned that unless the ban is lifted, "the majority of calves will have to be shot and the industry will face costs into the millions". So far, around 6,000 are believed to have been shot.
Haywood added that two weeks have passed since the last shipment of calves to leave Britain. A spokesman for the Defra said that it regretted the decision by buyers to stage an unofficial boycott. "There is a great deal of work being done by officials and the industry to provide reassurances to the Dutch and EU partners on this issue, to allow resumption of trade while minimising the risks of exporting TB-infected animals," he said.
The industry is trying to rebuild after severe restrictions were imposed in 1996, during the BSE outbreak.