A spokesman for Soil & Health, Steffan Browning, said the vaccine, which contains modified canarypox virus, posed big risks for the agricultural sector.
A public hearing was held by the Environmental Risk management Authority (ERMA) in Wellington yesterday to consider an application for conditional approval to use Proteqflu and Proteqflu Te vaccines.
The New Zealand Racing Board and New Zealand Equine Health Association seek approval to use it in the event of an outbreak, and on horses being exported to countries where inoculation with the vaccine is a mandatory import requirement.
Browning has raised the question of whether the vaccine's use might be compulsory as part of biosecurity efforts to contain any outbreak.
"In the event of an equine influenza outbreak, there is the possibility of the mandatory use of live GE Canary pox virus vaccine, even though farmers, lifestylers, horse owners and organic producers may lose markets that demand GE-free products," he said.
"ERMA must decline the application if it cannot ensure protection of the livelihoods and sustainable management choices of New Zealand growers."
Leaving such decisions to agriculture and biosecurity authorities is too risky considering a cost–benefit analysis could not be done comprehensively at the time, he said.
"Loss of GE-free status or organic certification and potentially leaving numerous GE contaminated sites throughout New Zealand for a short-term benefit for the racing industry is a task of ERMA's.
"Just as DDT, which was billed as a 'safe' solution to grass grub decades ago, but left long-term contamination and loss of land-use options, this GE flu vaccine will potentially leave contamination that cannot be cleaned up.
"In the event of mandatory use of GE canary pox virus vaccine against equine influenza, there must be a cost to the racing industry for the compensation of the thousands of horse and property owners that do not want their GE-free status tampered with.
"There are non-GE options and the racing industry and MAF-BNZ must ensure that quarantine and incursion event management is maintained at a high standard using the effective non-GE vaccines available already."
Soil & Health is opposed to genetic engineering in food and the environment.