Rodigan said that he was leaving Kiss FM "with great sadness", but also hit out at the "continued marginalisation of reggae music into the twilight zone of radio scheduling".
[David Rodigan pictured with Amy Winehouse at the Sony Radio Academy Awards in 2004]
The DJ's hour-long Sunday programme had aired at 11pm on Kiss FM.
A statement from the station said that it was "very sad and disappointed" to confirm Rodigan's departure.
"We have the utmost love and respect for David both personally and professionally," Kiss FM said.
"He leaves with our sincere appreciation and gratitude for all that he has achieved with Kiss."
Rodigan is a highly respected radio broadcaster, having been inducted into the Sony Radio Academy Hall Of Fame in 2005.
[David Rodigan receives his MBE from Prince Charles]
He was given an MBE in the 2012 New Year Honours for services to broadcasting, and this year won his third Sony Award for a different show on BBC Radio 2.
But in a statement on his own website, Rodigan said that Kiss FM had "left me no option but to make a stand for my passion".
"Due to their continued marginalisation of reggae music into the twilight zone of radio scheduling, it has left me no option but to make a stand for my passion and the music I love so dearly," he wrote.
"As Bob Marley famously said, 'The stone that the builder refused will be the head cornerstone'. Reggae was originally played on the streets, not on radio, and Kiss's refusal to schedule the only reggae show on their network to a socially accessible time has resulted in this decision.
"Reggae is worthy of more respect, and so are the fans and lovers of this music."
Kiss FM, which is owned by Bauer Media, insisted that it remained "passionate about broadcasting a brilliant cross section of music genres, including reggae".