Searchers will today concentrate on the Manukau Harbour mudflats from the air as hopes fade of finding a missing fisherman alive.

The 52-year-old father has been lost in the water for two days after his upturned aluminium runabout was discovered on Wednesday. Miraculously, his 8-year-old daughter was plucked confused and cold from the chilly harbour after Coastguard volunteers heard her calling in the darkness.

An extensive shore, sea and air search was mounted in the southern end of the harbour yesterday.

But this is being drastically scaled back and just the police Eagle helicopter will focus on the harbour at low tide today, due about midday.

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Yesterday Watersafe said it was unlikely the fisherman would be found alive if he was not wearing a lifejacket.

It is not clear how the pair came to be in the water or if they were wearing lifejackets.

The runabout was found yesterday afternoon and pulled out of the water at Weymouth, where the pair had entered the harbour.

Specialist child interviewers have been speaking with the girl, who was saved on Wednesday night after three hours floating in the Manukau Harbour.

Police have appointed a family liaison officer to support the family as the search for the father continues.