Wilkinson, representing the Wildlife & Countryside Link, said it was "imperative" to stop using peat because of the amount of carbon lost.
He told MPs last month: "There is greater value for the peat to remain where it is than being in my garden or yours. We have been pushing for a 2020 deadline. There is urgent need for the industry to act now because by 2030 there will probably be little peat left. The question will be obsolete by that point."
NFU horticulture adviser Chris Hartfield responded in the NFU horticulture board newsletter: "Comments made by Wilkinson were very disappointing. He effectively implied that all this peatland degradation was due to the extraction of peat for use in horticulture, when horticulture is one of the lesser threats facing peatlands."
He added: "If conservation organisations want to make serious progress towards environmentally-responsible and effective growing media, they need to look at the facts and stop demonising horticulture and gardeners over the condition of peatlands in the UK as well as globally."
When asked for clarification of his comments by HW, Wilkinson then said: "The Wildlife Trusts and the Wildlife & Countryside Link recognise that peat extraction for horticultural purposes is one of a range of factors causing degradation to peatlands in both upland and lowland areas."
He added: "We acknowledge the huge contribution gardeners are making to protecting wildlife in the UK and that the horticultural industry has already made significant progress in reducing its use of peat.
"We will continue working with the industry to ensure that the Government meets its target of phasing out the use of peat in horticulture by 2030."
But his reference to "upland bogs" also caused ire. Industry figure Graham Ward said: "Damage to upland blanket bogs is done by forestry, drainage, over-grazing and burning - not horticulture. This misrepresentation needs correcting."
Peat Timetable Clash over deadline
The 2030 date set to outlaw the use of peat in horticulture should be brought forward by a decade, the National Trust has told the Commons environment, food and rural affairs committee.
But NFU chief environment adviser Dr Diane Mitchell expressed significant concerns about the 2030 target because it was not scienceand evidence-based. It would also place a large cost on the industry, she said.
"We need to address the technical and economic challenges first. The concern from a UK perspective is that we should be peat-free at all costs."