This is according to farmers, exporters and analysts who said this on Friday, dimming hopes that they can make up ground after a slow start to the season.
The dry seasonal winds began to blow down from the Sahara last month, blanketing much of West Africa's cocoa-growing regions in dust, blocking out sunlight, and lowering temperatures.
The impact was visible in the world's top two producers, Ivory Coast and Ghana, but farmers in Nigeria and Cameroon said their light crop - which typically produces smaller, lower-quality beans - had not been affected.
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Farmers in top grower Ivory Coast said the Harmattan had hindered development of the April-to-September mid-crop.
"Last year at this time we had lots of flowers and cherelles (small pods) on the trees. But this year there's nothing," said Diedie Biali, who farms near the western town of Meagui.
Cocoa arrivals at Ivorian ports were around 11 per cent lower than last season's bumper crop by Jan. 11, according to exporter estimates.
"The latter half of the main crop is kind of a done deal. So whatever effect (the Harmattan) will have will be on the mid-crop," said Victoria Crandall, soft commodities analyst with Ecobank.
She said some exporters thought the Harmattan might simply reduce bean size. Others, however, predicted output losses.
"Our 2014/15 forecast was an overall decrease in the harvest size in Ivory Coast of 15 to 20 per cent, but with the Harmattan we think that drop will be bigger," an Abidjan-based exporter said.
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A European trader predicted a decrease in Ivorian output of 15 per cent, revising an initial forecast of a 10 per cent drop due to the Harmattan.
In No. 2 grower Ghana, where cocoa purchases were down nearly 23 per cent by Dec. 25 according to industry regulator Cocobod, farmers and buyers said the Harmattan could trim output by 20,000 to 50,000 tonnes.
"It has generated concerns among everybody, particularly the farmers," said one Ghanaian cocoa buyer. "But there is room for some recovery as the rains are about to set in."
A Cocobod official said the body would conduct a field assessment of the Harmattan's impact in February, before deciding whether to revise the Ghanaian production target of 850,000 tonnes of beans.
A spokesman for the Cocoa Association of Nigeria said the winds were not expected to impact output in Africa's No. 3 producer.
"We haven't noticed any damage to the trees," Godwin Ukwu said.
In Cameroon, the continent's fourth-biggest grower, farmers said trees had so far resisted the harsh conditions.
"If this situation goes on, that is until mid-February, it may destroy some of our plants and cut down production," said Emmanuel Nnogo Akolo, a farmer in the Centre Region, which accounts for 40 per cent of Cameroon's cocoa output.