The organisation, which represents organic farmers, said the National Farmers' Union (NFU) was putting economic considerations ahead of disease control.
The government is trying to persuade farmers to back its plan to vaccinate thousands of cattle to stop the spread of the epidemic.
This is despite food experts insisting meat and milk from vaccinated animals is safe.
The Food Standards Agency (FSA) and the National Consumer Council have said there would be no risk from eating or drinking products derived from vaccinated livestock.
The FSA said more than 30 common vaccines were already being used in modern livestock farming without any harm to the food chain.
Soil Association director Patrick Holden said the NFU's attitude towards vaccination was hypocritical.
"They (the NFU) have been responsible, directly and indirectly, for promoting livestock production systems which are heavy users of drugs such as antibiotics and vaccines, that get into the food chain on a regular basis," he said.
"Here is the Soil Association, which is normally associated with promoting safer products, saying in this case vaccination is perfectly safe."
Penalised
The SA added that opposition to vaccination could be because there was already a good compensation package on offer for farmers who lose animals.
Many organic farmers feel penalised by the current policy of slaughtering animals to halt the spread of foot-and-mouth.
It takes them much longer to re-establish their livestock herds with organic status but they receive no extra help.
On Thursday, NFU president Ben Gill reiterated his opposition to vaccination.
Mr Gill said he had written to his union's local offices explaining why the leadership did not think vaccination was desirable.
"Remember, once you start vaccinating, you can't say 'Let's stop and go back to where we were'.
"You are committed. Animals have been exposed to the vaccine and hence the consequent problems," he said.
'Ironic'
A spokeswoman for the NFU said the SA's arguments did not stand up.
"It says we are putting economic considerations ahead of disease control, but even the government's own scientists don't regard the vaccination programme as a disease control measure.
"It is designed to ease pressure on resources."
Responding to the accusation of hypocrisy, she said the same could be said of the SA.
"It is ironic that the SA is quoting the advice of the Food Standards Agency (FSA) on the safety of meat and milk from vaccinated cattle.
"The FSA relentlessly campaigns for genetically modified organisms, something that the SA is totally opposed to."