Two men accused of beating a seal pup over the head with an oar say they had no humane alternative.

In an exclusive interview, Matthew Botica, 22, and Tomoare Angoika, 39, have pleaded for public sympathy after injuring the young fur seal so badly that it had to be put down.

The two appeared in Waitakere District Court this week, where they pleaded not guilty to violating the Marine Mammals Protection Act.

Botica admitted that he struck the young seal multiple times on the head after it became tangled in his fishing net, but said he had no choice because he did not have a knife to cut the net.

The pair had been mullet fishing in a Henderson creek, and were arrested after passersby called police. The injured animal was taken to Auckland Zoo and later euthanased.

"I just wanted to get it out of the net," Botica said. "It started barrel-rolling and getting more tangled up. It would try to bite my hands, at one point I almost fell in. It could have capsized the boat."

Botica said he tried to free the seal for more than 20 minutes before they decided to strike it with the oar.

"It started getting erratic and vicious. All I did was just grab one of the oars and I was using the flat part to hit its head. All I wanted to do was just to stun it so it would stop wriggling.

"I tried to hit it a couple of times but we were getting nowhere. We went to the water's edge and it made it worse for us because it had a lot more movement out of the water. Tomoare tried to take it by hand and it sort of ran at him. It was going for him. Then he grabbed the oar and he hit it and by then it was quite stunned."

Botica said they left the unconscious seal on the bank so it would be safe from the incoming tide.

When questioned about whether the pair had thought to let the seal get itself out of the net, Botica said it would have been "impossible".

"If we had left it, it would have lost its energy and just drowned."

His solicitor Zeljan Unkovich added: "They did what they thought was reasonable and they were also influenced by concern for their safety. They might not be the sharpest tools in the shed, but they haven't gone out there to bash up a seal." Botica believed the charges were unwarranted.

"I think the reason they're taking me to court is wrong. They don't need to give me a conviction [for] that, it's just wrong," he said.

When asked if he was sorry for what was done, he replied: "Yeah, I didn't want any of this to happen."

Botica has run his family's West Auckland timber company since his father died two months ago. The business employs nine staff including Angoika, a father of six.

Unkovich said while Angoika had a previous conviction related to a domestic assault, Botica had no criminal history.

"One of the reasons they were fishing was so Tomoare could have fish for his family because things were tight."

The pair have funded their own legal team.