Despite New Zealand signing a sweeping new agreement on military co-operation with the United States, its anti-nuclear legislation is the reason two navy ships have been refused entry to Pearl Harbour during the world's largest maritime exercise.

For the first time in 28 years, the Defence Force is taking part in this year's Exercise Rim of the Pacific, known as Rimpac. The force has proudly publicised New Zealand's involvement in the US-hosted exercise.

The frigate Te Kaha and Auxillary Support Vessel (fuel tanker) Endeavour are in Hawaii, along with a rifle platoon from the Infantry Regiment, a counter-mine team, an air force P-3K Orion and a dive team based in San Diego.

The ships made front-page news in Honolulu, with the local Star-Advertiser reporting New Zealand was the only country "refused entry" to Pearl Harbour.

Prime Minister John Key said there was "nothing new" in the United States' position.

"That's been the position since the (nuclear-free) legislation was passed in 1987."

It did not affect the exercise which was being conducted out at sea.

"They're just in another part of the port, the commercial part, we're not surprised, we thought that might happen," Key told TV3.

The new agreement was a "step forward" because it recognised the laws of each country.

But the nuclear-free issue was a rock in the road that both sides had agreed to get past, Key said.

"We would need to either change our position of the US Navy would need to change its position around confirm or deny and I don't think that's going to happen on either side."

The exercise was still worthwhile, he said.

Defence Force spokesman Major John Gordon said the two ships were berthed at Aloha Towers, which is in the tourist part of Honolulu Port.

"They are not stationed within the actual harbour itself."

Defence Minister Jonathan Coleman said refusing New Zealand ships at naval ports was a longstanding US policy enacted after nuclear-free legislation was introduced in 1987.

"I understand there have been some exceptions in the past but this is nothing new." New Zealand was not prepared to change its policy and so had not expected the US to change its policy, he said.

"The reality is we're getting all the military engagement benefits as it is, so where the boats tied up is not really a big deal to us at all."

The Rimpac exercise was happening at sea, so it was not affecting New Zealand's involvement.

The Washington Declaration was signed by Coleman and US Defence Secretary Leon Panetta last month. It agrees on closer co-operation in areas including maritime security, counter-terrorism, humanitarian assistance and disaster relief.

- © Fairfax NZ News