Two management options for pathogens P. ramorum and P. kernoviae have been put forward as part of the consultation, which ends tomorrow (10 October).
Meeting minimum EU requirements on control of P. ramorum and removing all controls against P. kernoviae is one option - estimated to cost £46m over 20 years.
The second, cheaper option (£32.2m) is to increase control by enhancing containment and eradication measures at nurseries and garden centres, and continue removing hosts of the diseases, especially Rhododendron ponticum, in woodlands and gardens.
Defra scientist Gordon Friend told delegates at a Stoneleigh meeting last week: "Though the first option would mean a cut back on the number of government inspections, other costs would then increase."
The other costs would result from an export ban of susceptible plants, increased levels of disease in the nursery trade and increased infection of trees.
Stockbridge Technology Centre science director Dr Martin McPherson said: "I would question the figures - it's a long list of assumptions. I find it difficult to believe that option two will be cheaper than option one. And we also can't assume we can control it."
Rhododendron grower John Middleton said: "The first option would allow the spread of a notifiable organism, P. kernoviae, not present in other EU countries to spread throughout the UK, leading to an embargo of exports from the UK.
"The second option would allow the continuation of the current destructive policy in an increased form to gardens and nurseries because of an undetectable organism that has not been proven to have killed a single tree since its detection in Europe in 1993."
John Woods Nurseries' representative Malcolm Dick said: "We fully support measures being in place. But having said that, neither option is satisfactory. What research has been done?"
And post-doctoral research assistant Ralph Desimone from Cambridge University said: "I was curious to see what research they are doing into the control of the pathogen but we didn't see anything today about how they are controlling the disease in woodlands."
Government ministers will decide on the management of Phytophthora within the next three months and aim to implement the strategy by spring 2009.
Outbreaks of P. ramorum (Apr 2002-May 2008)
Nurseries and garden centres 601 (510 sites)
Managed/unmanaged land 227 (204 sites)
Outbreaks of P. kernoviae (Oct 2003-May 2008)
Nurseries and garden centres 4 (4 sites)
Managed/unmanaged land 54 (54 sites)