A timber exporter has been ordered to pay $100,000 in freight charges for timber lost in the Rena grounding, despite the Middle East-bound load not making it to the destination.

The High Court has ruled Resources New Zealand Ltd must still pay its freight bill to the ship's charterer at the time of the grounding - Mediterranean Shipping Company.

Timber strewn across Matakana Island in the months after the Rena hit the reef.

Resources NZ had argued it was 'unjust” to make it pay MSC, given its sawn timber did not make it from Napier to its markets in the Middle East, reports Stuff.co.nz.

The ruling comes more than two years since the Rena cargo ship grounded on Astrolabe Reef on October 5, 2011.

Resources NZ's shipment made it only to the Bay of Plenty.

Resources NZ had not established it should not pay the $101,306.26 MSC invoice, a finding in the High Court in Auckland by Associate Judge David Abbott said.

MSC confirmed that in early 2012, when Resources NZ queried whether it still applied, given the Rena had sunk.

Despite this, MSC took legal action demanding the invoice be paid last July, 21 months after loading the timber.

Resources NZ said it disputed the debt, as the contract implied the goods would be delivered safely.

Associate Judge Abbott said the contract was clear and unambiguous. Those involved were commercial parties familiar with such contracts, and there was no suggestion the contract was not entered into freely.

It was clear freight was payable, said Associate Judge Abbott.

Risks such as the ship sinking were known, as was the ability to protect against such losses with insurance.

'The circumstances of the grounding of MV Rena and loss of its cargo were unfortunate, but do not make this transaction, or the claim for freight and the ‘no set-off' clause extraordinary, so as to make it unfair to require Resources NZ to adhere to the terms of the contract.”

Associate Judge Abbott ordered Resources NZ to pay MSC its costs.