"The lack of clarity from the Government at the moment is very concerning," Kirsten Pullen, chief executive of the British and Irish Association of Zoos and Aquariums (BIAZA) told the Press Association.
Withdrawal from the EU without a deal in place could mean Britain is forced to leave European Endangered Species Programmes.
It would then have to negotiate deals country by country, a time consuming process that could leave species with short life spans and limited breeding cycles vulnerable, Pullen warned.
Species that have benefited from the programme recently include rare Sumatran tigers, Indian one-horned rhinos and elephants.
"It is hard to pinpoint a particular species within our breeding programmes because all of them could potentially be impacted if we suddenly can't deal on a European basis, or it's much harder to deal on a European basis," Pullen said.
She added, however, that it could create "potential for opportunity", as Britain could find it easier to work with countries like Australia and the United States once outside the bloc.
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