The South American country is the largest producer of cocaine in the world, and much of it is destined for the US market.
Duque said that 94,000 hectares (232,000 acres) were destroyed manually -- with machetes and similar tools -- out of a total of 100,000 hectares destroyed.
"I want to highlight the work of the public labor force, which managed to manually eradicate the largest amount that our country has seen in that way," said Duque, who did not give a figure for the previous record.
According to the United Nations, 169,000 hectares of coca leaf were planted illegally in Colombia in 2018, enough to produce 1,120 tonnes of cocaine.
Duque said 434 tonnes of cocaine were confiscated in 2019.
Colombia aims to reduce by half its illegal coca leaf plantations by 2022-23.
Duque was elected president in August 2018 on the back of a pledge to come down hard on drug-trafficking.