Two boaties were rescued overnight after having motor difficulties off Wellington's south coast.

Police, Westpac Rescue Helicopter, Coastguard and Airport Marine Rescue were involved in helping the men in what police said were "rough conditions".

A man spotted the pair having motor difficulties with their 2.5m dinghy about 5.40pm and called police.

They were drifting about 100m from the shore at Red Rocks.

However police were unable to get an exact location for the stranded boaties and the Police Martime Unit could not find them in an initial search from Sinclair Head to Owhiro Bay.

"We were really concerned for their safety. There was a very strong offshore wind making conditions challenging and there was a real possibility that they may have capsized," Maritime Unit supervisor Sergeant Richard Kennedy said.

Kennedy said the pair were blown towards the outermost rocks at Sinclair Head about 300m from the mainland.

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"They managed to scramble up the rocks and drag their dinghy up with them."

​Kennedy said​ one of the men had a cellphone in a plastic bag, which stayed dry.

About 6.40pm the maritime unit saw the men standing on the rocks at Sinclair Head.

"It was too dangerous to rescue the men by boat, so police directed the Westpac Rescue Helicopter to their location," Kennedy said.

"Despite the trying conditions, within half an hour both of the men had been winched off the rocks to safety in a fantastic effort from the rescue helicopter crew."

The two men were cold and wet but uninjured.

"The men were incredibly lucky they made it onto the rocks as finding them in the water could have been extremely difficult in rough conditions," Kennedy said.

The men were wearing lifejackets.