The New Zealand navy was involved in a high-seas standoff with two suspected poaching ships in Antarctic waters Wednesday after the vessels used "evasive tactics" to thwart boarding attempts, officials said.

Foreign Minister Murray McCully said the naval patrol vessel HMNZS Wellington had been monitoring three "illegal fishing vessels" in the Southern Ocean this week which were sailing under the flag of Equatorial Guinea.

He said authorities in Guinea believe the ships Yongdong, Songhua and Kunlun are operating illegally and have given the New Zealanders permission to board them.

"The HMNZS Wellington attempted to exercise its legitimate right to board the Yongdong and Songhua earlier today but the vessels refused to cooperate," he said in a statement.

"Due to the conditions and the evasive tactics of the masters, it was not possible to safely board these vessels."

McCully said New Zealand had strong evidence the vessels were involved in illegal fishing, even if the navy could not get aboard to check their records.

"What we have already achieved is significant photographic evidence of what these guys have been up to down there," he said. "This is cynical international criminal activity and we need to stamp it out."

While the ships are flying the colours of Equatorial Guinea, McCully said investigations suggested they were linked to a Spain-based syndicate.

He said New Zealand had asked Interpol and Spanish authorities to conduct further enquiries.

The vessels are operating in a protected area regulated by the Commission for the Conservation of Antarctic Marine Living Resources (CCAMLR), a multi-national body.

They are believed to be targeting toothfish, also known as Chilean sea bass, a deep-water fish popular in expensive restaurants.