The rule – effective from 1 April – does not apply to horses jumping in BS club competitions (who compete for points, not prize-money) or those that are already registered with BS.
But critics say the decision will affect those who want to jump older horses at the lower levels, as most young horses are now chipped as a matter of course.
Robert J Twiddy, director of Sports Horse World – which breeds KWPNs – told H&H the change was “not needed”.
“I have no problem with microchipping if it were dedicated to grade As competing for the larger prize-money,” he said.
“What I object to is retrospectively asking us to microchip a 13-year-old horse who is jumped for pleasure at the lower levels.”
Mr Twiddy – who had been planning to reregister his horses with BS – believes the cost will cause a “backlash” from owners who have several horses.
“At £50 per horse, this runs into a great expense on top of what are becoming expensive BS fees,” he added.
BS members have also claimed that the amendment was “buried” in the rulebook. Others have said they will jump on a day ticket rather than reregister.
But BS chief executive Iain Graham defended the decision, saying it was an “identification” issue.
“It helps us and the members know that the horse in the ring is the horse that is registered,” he said.
BS stewards will carry out spot checks with scanners at shows throughout the year.
Mr Graham added that no one who wanted to jump affiliated should be deterred by the cost of microchipping.
“We are running chipping and vaccination days [flu vaccinations are compulsory for all BS horses from 1 April] around the country.
“People can bring horses to central venues so there’s no vet’s call-out fee,” he added.
BE says it expects to hold discussions “this year” to consider whether its rules need to be amended, while a BD spokesman said the rule “would come in eventually”.
This news story was first published in the current issue of H&H (26 January 2012)