The foot-and-mouth epidemic has cost the United Kingdom's three zoos with close university affiliations more than £1.5 million.
Research activities at Bristol Zoo Gardens may be hit by a £200,000 loss of business following a month's closure.
But both Edinburgh Zoo and the Zoological Society of London are confident their research budgets will be unharmed.
Sharon Redrobe, Bristol's zoo veterinary officer, said research might suffer "because it is not as essential as funding the animals and retaining staff".
Seven species of animal thought susceptible to foot and mouth, including okapi and tapir, have been moved to a secure site owned by Bristol Zoo.
But a 41-year-old Asian elephant called Wendy has had to remain locked inside her shed at the zoo as moving her might be hazardous and there are no appropriate facilities to care for her elsewhere.
London Zoo has stayed open, while sister site Whipsnade closed for almost two months.
The Zoological Society of London expects to lose up to £1.25 million as a result.
But Georgina Mace, director of science, said research expenditure was externally funded and the losses would not affect this.
Despite losing £170,000 after five weeks of closure, Edinburgh Zoo also does not expect its research activities to be affected.
However, the threat of disease has prompted the removal of one species, maras, to another site and 14 others, including hippos, giraffes and zebras, have been barricaded from the public.