Heavy, persistent rain over 36 hours has cost Central Otago cherry growers millions of dollars in yet-to-be-picked fruit.

While damage was still being assessed some growers estimate losses at between 30 per cent and 60 per cent and more rain is forecast.

Growers in Earnscleugh, near Clyde, took advantage of a brief reprieve from the rain yesterday morning to assess the damage to what were bumper crops in a season plagued by concerns about labour shortages.

The area was one of the hardest hit by the rain which began on New Year's Day and did not let up until about 8.30am yesterday, causing the Fraser River to breach its banks coupled with localised runoff from the hills.

This led to the closure of Earnscleugh Rd and Strode Rds late on Saturday and fruit trees in the area being inundated by up to a metre of flood water.

Panmure Orchards owner Jeremy Hiscock said the prognosis for cherries was not good.

"It's tough to be a cherry grower. The rain is devastating for the whole region."

He had measured 88mm of rain over the 36-hour period and that was unusual.

"We usually have a lot of heavy rain over a short period or a long period of light rain. This time we had both — a lot of rain over a long period."

Hiscock's wife Bridget said the water had ripped through their property, flooding sheds and forcing workers to higher ground.

"We had them camping on the road and on our concrete pad."

Cherries were hardest hit but she feared for other trees, such as nectarines still standing in water, yesterday.

Damage was still being assessed. Some varieties of cherries had fared better than others.
"There are some varieties that are not rain tolerant."

Some varieties were a "total loss", Hiscock said.

The issue was the fruit taking in more water than it could handle, causing it to swell and crack. "They look like hot-cross buns."

It would probably be Wednesday before he could get pickers in and assess the damage — that could mean abandoning entire blocks of cherries that were no longer viable to pick.

"It is fair to say there is significant damage throughout the whole region."

The irony was after labour shortages had largely been addressed, some growers could be forced to lay off staff dependant on crop losses, he said.

"It's not just the growers but the community that depends on that industry."

Wednesday was also set as the starting point for other growers throughout Central Otago and most said they had yet to assess the damage.

Near Cromwell, Suncrest Orchard owner Michael Jones was taking that approach.

"It's not going to be good."

Sunfruit Syndicate Limited Partnership shareholder Tim Paulin estimated 30 per cent-60 per cent damage across his cherry crops between Cromwell and Clyde.

"I've never seen rain like it."

Teviot Orchard Company owner Gary Bennetts said he measured 90mm of rain over four days at his orchard near Roxburgh.

"There'll be a bit of damage. I'll go and have a look at them tomorrow [today]."

Central Otago produces about 90 per cent of New Zealand's cherry exports, which were worth $84.1million in the 2017-18 year and $66.2million in 2018-19.

Former Orchardist and Central Otago Labour Market Governance Group chairman Stephen Jeffery said based on those figures even a 10 per cent reduction in this season's harvest would shave millions of dollars off the Central Otago cherry industry.

"But people are still tallying losses. It is pretty difficult to say, and there is more weather to come."