Riders must keep to tight limits on the number of times they strike a horse but will now be able to use that allocation at any point in the race.
Jockeys could still lose prize money for infringements and representatives said “serious concerns” remained.
The ruling comes into force immediately and will be applied retrospectively.
Flat jockey Adrian Nicholls, who was given a five-day ban at Pontefract on Monday for whip offences, has welcomed the changes, which maintain the new limit of seven uses of the whip in Flat races and eight over the jumps, but lift the specific restriction of five strikes in the final furlong or after the last obstacle.
“I’m glad that common sense has prevailed,” he said. “I thought they were very harsh rules. I think the new rules are better for racing.
“The amount of times was never an issue with me, it was more the hefty bans and the financial penalties. Hopefully now we can put this behind us and concentrate on the good bits about racing.”
However, the Professional Jockeys’ Association (PJA) which accompanied a delegation of riders to a discussion with the BHA on Monday, said “serious concerns” over penalties remained.
“There are still serious concerns about the level of penalties for minor infringements of the rules,” PJA chief executive Kevin Darley said in a statement.
“A jockey could still be in breach of the rules and face a heavy penalty for using the whip in the best interests of safety and horsemanship.
“There are also concerns about the way the rules may impact differently on Flat and jump racing.”