The row over business rates is the latest in a series of criticisms of the Uniform Business Rate, which is likely to impose sharply higher bills on businesses outside the South-east because commercial rents, on which the rates are based, have risen since the last revaluation five years ago.
Business tenants in the South have also launched a strong attack on a planned transitional relief scheme, which means that reductions in their bills forecast because rents have fallen over the past five years will not be passed on in full.
John Harris, the federation's chairman, said it was absurd that shopkeepers who fitted shutters or security cameras on their premises to combat burglars and ram raiders, should then be penalised for it.
"Why should people have to pay additional tax when all they are doing is trying to combat crime?", he said.
"It shows that the whole system of rating is fundamentally flawed. Most of these figures are just `lick your finger and stick it in the air' valuations anyway."
The federation is encouraging small businesses to contact their MPs and push for security measures to be excluded from the rates valuations.
The new ratings are due to come into effect from the beginning of April, replacing the 1989 valuations.