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 was last seen in the North's state media last December at the death anniversary of the late leader Kim Jong-Il, South Korea's unification ministry said today.
Seoul was "closely monitoring the possibility of any changes in Choe's circumstances", said the ministry, which is in charge of cross-border affairs.
Such a violent method of execution has been cited in various unconfirmed reports as being reserved for senior officials who the leadership wished to make examples of.
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The North has not officially confirmed Hyon's execution -- reported in May by Seoul's intelligence agency -- but announced his replacement, Pak Yong Sik, in July.
The South's spy agency also claimed in May that Kim had executed dozens of officials -- including his own uncle -- since taking power after the death of his father in December 2011.
Kim, believed to be in his early 30s, has repeatedly reshuffled senior army officials in a move analysts say was aimed at forcing them to remain loyal to the young ruler.
The Kim dynasty has ruled the impoverished and isolated North for more than six decades with an iron fist, a pervasive personality cult and almost no tolerance for dissent.