Daily bean arrivals at Makassar port have dropped to around 100 tonnes from 200 tonnes in the previous week. The harvest is expected to dwindle through December.
Traders have said floods, rampant pests and ageing trees yield less cherry in Indonesia, the world's third largest cocoa grower.
"I wouldn't be surprised if the crop declines dramatically compared to the deliveries I had last year in South Sulawesi," said one trader with a major trading firm in the provincial capital of Makassar.
"Quality is not such a bad issue, but in terms of volume it's not looking good," he added.
On the quality side, traders said bean counts had improved and were 5 beans more than the standard count at 115 per 100 grams, against 120 beans per 100 grams at the beginning of the harvest last month.
"You still have small amounts flowing in but very slow, very low arrivals," said one Singapore trader.
The mid-crop is much smaller in size and is harvested from October to December. The main harvest runs from May through August on Sulawesi Island, which accounts for 75 percent of Indonesia's production.
Lower output and higher production costs are expected to narrow differentials to New York futures to $220 a tonne in the near term.
On Tuesday, differentials were quoted flat from last week at $235-$245 a tonne below New York futures for March, which shed $4 to $1,409 a tonne on Monday.