East Herts District Council has recommended the plan for refusal.
A Waitrose representative said: "Van Hage has withdrawn its application in light of the officers' report and to allow further consideration of the scheme before resubmitting at a later date.
"There were certain matters, particularly highways, that Van Hage felt could be positively resolved, however this was not possible by the meeting of the planning committee.
"Council officers would not agree to a deferral to allow these matters to be resolved so Van Hage were left with no choice but to withdraw the application."
Managing director Chris Roberts has said the Waitrose, planned to open in spring 2016, would "guarantee the future of the site"..."and could be a model for garden centres going forward".
Notcutts withdrew from a £14m joint-location plan with Waitrose this year at Bagshot after its financial feasibility studies and concluded that a garden centre would not be viable because of too much local competition.
But at Wyevale Garden Centre’s Percy Thrower Centre in Shrewsbury, building contractor Speller Metcalfe began work on a rebuild of the centre and construction of a neighbouring Waitrose on site in June.
WGC said a date has yet been announced for completion.