Radio 4 said the show had drawn a steady 1.4 million listeners a week for the past five years and often nearly topped audience popularity polls.
It was stung into action after Buczacki slated the show in an article for the Daily Mail. He accused it of being a "pathetic shadow of its former self".
He said it had been in steady decline after "the rot set in" in 17 years ago when it was sold to an independent producer who forgot the adage "if it ain't broke, don't fix it".
Buczacki added: "Now, in the hands of company Something Else, which also produces pop and hip-hop shows, Gardeners' Question Time no longer offers any sense of location or identity. Panellists seem to be nomadic creatures of no fixed abode."
Radio 4 insisted that the horticultural content of the show remained strong, with the same amount of time devoted to questions and answers as in the past.
Buczacki, a former panellist and chairman of the programme, took part in 600 episodes without a break for 13 years until 1994.