A large container ship heading from Napier has hit a reef near Tauranga this morning flooding two cargo holds.

The 236 metre cargo vessel Rena was heading from Napier to Tauranga when it crashed into the Astrolabe Reef, about 6 nautical miles north of Motiti Island at about 2.20am.

Two cargo holds were reportedly flooded but tanks containing the ship's heavy fuel oil were undamaged, and the ship was on a 12-degree lean, said a Maritime New Zealand spokesman.

There were no reported injuries to the 25 people onboard.

A flight over the area was being coordinated by Maritime New Zealand and the Bay of Plenty Regional Council to assess if anything was leaking from the vessel.

A team of trained spill responders and Maritime Incident Response Team were monitoring the site.

Maritime NZ was working with the crew, and a safety inspector was onboard assessing the damage.