Choe, who took the job in June 2014, was executed by firing squad in May after voicing opposition to forestry policies promoted by Kim, Yonhap said, citing the source "with knowledge of the North".
Choe has not been mentioned in the North's state media since last October, it added, in another apparent sign he had been purged.
Choe's death, if confirmed, would be the second reported this year.
Defence minister Hyon Yong-Chol was said to have been executed in April by anti-aircraft fire for insubordination and dozing off during formal military rallies.