Two men accused of bashing a fur seal which was later put to death, say they will deny criminal charges.

Tomoare Angoika and Matthew Botica appeared in Waitakere District Court today on charges laid under the Marine Mammals Protection Act, after a seal pup found in a west Auckland creek in January had to be put down due to its injuries.

Their lawyer Steve Bonnar said outside the court the pup was hurt and the two men were trying to extract it from the net and stop it drowning.

He said it was not a case of cruelty and the men were "distressed and upset" to learn the injured pup had been put down.

He said they did not intend to injure or kill the seal.

The men will be back in court in September.