Output is already expected to drop by a third in the fourth quarter of this year, also due to heavy rains. The cloud cover that comes with bad weather can also damage the flowering of coffee trees.
"We can be sure that we will have a fall of 20 percent in the first half," Roberto Velez, the head of the national growers federation, told journalists, noting that rains in July, August and September had damaged the flowering of trees to be harvested in 2018.
The country produced 6.37 million 60-kg bags in the first half of 2017.
Output for this year will be below a previously predicted 14 million bags, Velez added.
"It would not surprise me if we finished this year with production of between 13.8 and 13.9 million bags. The months of October, November and December have been very poor."
Colombia produced 14.2 million bags in 2016.
The country missed its production target from 2009 until 2012 because of heavy rains and a tree renovation program that took some fields out of production. More than half a million Colombian families make their living from coffee farming.
The government hopes to increase yearly production to 18 million 60-kg bags through tree renovation and substitution of coca, the raw ingredient in cocaine, for coffee.