The captain and second officer of a ship that caused New Zealand's biggest sea pollution disaster were deported to the Philippines Thursday after completing half of their seven-month jail terms.

The Liberian-flagged Rena ploughed into an offshore reef in October last year, releasing an oil slick that killed thousands of sea birds and fouled beaches in the North Island's pristine Bay of Plenty.

Captain Mauro Balomaga and navigator Leonil Relon were both jailed for seven months in May after pleading guilty to charges including operating a ship in a dangerous manner and attempting to falsify navigation records.

The pair were released on Wednesday and Immigration New Zealand confirmed they were deported to their homeland in the Philippines Thursday morning.

The Rena hit the Astrolabe Reef 22 kilometres (14 miles) offshore in clear conditions as it steamed at full speed towards Tauranga, New Zealand's largest container port, becoming stuck on the submerged rocks.

More than 300 tonnes of toxic fuel oil spewed from the vessel, creating an oil slick kilometres long that washed onto beaches at the popular tourist spot, coating birds in thick black sludge.

Environment Minister Nick Smith described it as New Zealand's worst maritime pollution disaster.

The government has estimated the disaster clean-up will cost NZ$130 million ($103.6 million), most of which will be covered by the Rena's owner, the Greece-based Costamare Shipping Company, and its insurers.