A young seal that went under a railway carriage for a sleep only to have a flipper crushed when the wagon began moving is back in the wild after surgery.

The 10-month-old male pup was left with three bones protruding from his back flipper after the accident, at KiwiRail's Otahuhu shunting yards last Thursday morning.

KiwiRail staff had tried to shoo the animal back into the Manukau Harbour the previous night, but he returned to the yard, settled underneath a wagon and fell asleep.

"He probably just thought it was a nice, warm place to sleep," Auckland Zoo veterinarian John Potter said.

Centre for Conservation Medicine staff removed bones from four of the seal's toes, then sutured the skin closed over it.

"He had quite a bit of flipper removed," said Mr Potter. "He's left with about a third of it."

Mr Potter said this would not disadvantage the pup in the wild.

Seals propel themselves through the water with their front flippers, and their back flippers used mainly for steering and grooming.

"He's left with a rudder to guide his way," Mr Potter said.

Conservation Department biodiversity programme manager Andrew Nelson said fur seals were often injured by sharks, boat propellers and fishing nets.

"We're fortunate with this guy that we've been able to watch him and bring him here. His mobility seems to be quite good, and he's quite a robust creature."

The seal was released at Whatipu yesterday. Nelson said it was uncommon for seals to travel so far up the Manukau.