September London cocoa slipped 0.1% to 1,609 pounds per tonne.
July raw sugar rose 1.9% to 17.70 cents per lb, having settled down 1.9% on Monday.
July arabica coffee rose 0.3% to $1.6055 per lb, having settled down 1.5% on Monday, extending its retreat from last week's 4-1/2-year high of $1.6675.
At this time in 2020, coffee farmers in the world's largest producer had collected 23% of the crop. The 5-year average for this time of the year is also 23%.
Safras projects a crop of 56.5 million 60-kg bags in Brazil this year. The government has estimated a lower figure of 48.8 mln bags.
Safras now expects the harvest of arabica beans to reach 34.7 million bags versus 35.2 million bags previously. Compared to last year's crop, the reduction on arabica production is 31%.
The consultancy adjusted slightly upwards its projection for robusta coffee production in Brazil by 100,000 bags to 21.8 million bags. The Brazilian robusta crop is seen growing 12% from last year.
International arabica futures prices are on a tear at the moment, trading near four-year highs mostly because of falling output in Brazil, which accounts for up to half of the world's arabica supply.
"(We've) been having labor shortages over the last couple of harvests. Low prices play a role, its hard to improve wages," Juan Luis Barrios, president of Anacafe, told.