Growers such as Coletta & Tyson in Humberside and others in the West and Midlands suffered "severe effects", Stewart said - and many are still clearing debris the floods have left.
The European Commission has announced that EUR162.4m (£128.2m) from the European Union Solidarity Fund will help deal with the "consequences of devastating floods" that hit the UK last summer, but none will go to growers and farmers.
Stewart said: "Growers are taking on responsibility for keeping drains and watercourses clear themselves. That's expensive and time-consuming."
He added that the problem was "not of the highest priority for councils" and that garden retailers hit by sales downturns during the flooding would never be compensated.
NFU vice-president Paul Temple said: "Farmers and growers bore significant costs and disruption during last summer's floods with estimates of almost 50,000ha being flooded."
Sir Michael Pitt's review of the summer floods released last week found that local authorities and the Government have learned nothing from the devastation. The HTA said councils must recognise the importance of planting in flood defence.
The report makes 92 recommendations, including putting the army in charge of response, improved flood-warning systems, new building regulations and better protection of critical infrastructure sites.
- See www.cabinetoffice.gov.uk/thepittreview.aspx.