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Bosses at Bristol Zoo Gardens have launched an investigation into what happened.
It has been alleged that a senior animal keeper lashed out at the South American fur seal, which belongs to the same family as sea lions, when handlers tried to weigh it and it refused to co-operate.
A source told The Sun: "The keepers were weighing the sea lions. The senior keeper had taken one off the scales and put the next sea lion on - but the junior keeper forgot to recalibrate the scales.
"As he went to take it off the sea lion then put its flipper on the scales and it is alleged the senior keeper hit it."
The zoo's head vet has examined all of the seals at the popular tourist attraction and they remain on public show in their enclosure.
A Bristol Zoo Gardens spokeswoman said: "A senior animal keeper at Bristol Zoo Gardens has been suspended pending further investigation of an alleged animal welfare incident that has recently come to light.
"As this is an ongoing investigation, Bristol Zoo is currently unable to discuss the details of the incident.
"However, the zoo has acted rapidly and comprehensively by instigating an immediate, formal and extensive investigation in line with its internal policies and legal welfare requirements.
"Michelle Barrows, head of veterinary services, has examined the seal family and all individuals are behaving normally, engaging happily and playfully with keepers and guests in their enclosure.
"The animal has been, and continues to be, on full public show.
"Bristol Zoo would like to make it very clear that it has a zero tolerance towards such behaviour and takes its commitment to the highest standards of animal welfare and conservation seriously."