Johnson was chiefly held accountable for running a horse, Striking Article, eight times after he had undergone a palmar neurectomy, and for which he was banned for three years.
The procedure involves severing nervous connection to the lower leg to cause numbness. It is banned under the Rules of Racing on welfare grounds.
Johnson, 58, claimed he was unaware of the rule stating he should not have run the horse.
The neurectomy to Striking Article’s left-foreleg came to light following a post-mortem carried out after the horse was pulled up and euthanised at Musselburgh on February 7, 2010.
Striking Article underwent the procedure in April 2008 yet ran eight times afterwards.
Johnson was also charged under a separate investigation in relation to the administration of laurabolin, an anabolic steroid containing nandrolone, to three other horses. He was banned for one year in relation to those charges.
Johnson, whose principal owner is former Sage computer magnate Graham Wylie, has held a licence since 1984, and resides at White Lea Farm, Crook.
Wylie has already transferred six of his horses to champion trainer Paul Nicholls’ stables in Somerset, although that was reportedly unconnected with the Johnson hearing.
Johnson and Wylie’s most noteworthy victories have revolved around the fine staying hurdler Inglis Drever, three times a winner of the Ladbrokes World Hurdle at the Cheltenham festival.
A statement from the BHA disciplinary panel said that at the outset of the hearing Johnson had admitted being in breach of the rules stating he should not have run Striking Article.
It also said that Johnson’s position was that the declarations were made in circumstances where he was not aware of the prohibition under the rules.
It said that Johnson accepted that, by being unaware of the Rules of Racing that prohibited the declaration of horses to run in races that had been subject to a neurectomy procedure, he did not fulfil the requirement that he conduct his business of training racehorses with reasonable skill and care.
The panel said Johnson made no admissions in respect of the anabolic steroid charges.
Johnson indicated when contacted that he has no plans to appeal the suspension and that he intends to retire from training. He plans to issue a full statement early next week.
Wylie said: “I’m absolutely, totally shocked. Howard has been treated like a criminal and he is not.
“I think it’s a disgusting decision and I’m disappointed for Howard.
“I just feel so sorry for him because that is not Howard and he looks after his horses incredibly well. He would never do anything to harm a horse.
“I think they (BHA) have come down too heavy handed for the charges that have been made against him.
“It is a very sad day for northern racing as it has lost a very good trainer and they have also lost a very good owner.
“Most of my horses will go the sales and the rest of those that I keep will either go down south to be trained or to Ireland. I shall spend the weekend thinking about it.
“It’s a very sad day.”
Paul Struthers, head of communications for the BHA, said: “The Authority is satisfied that the Disciplinary Panel has imposed a significant and appropriate sanction for what were two different but very serious offences.
“A four-year disqualification means that Howard Johnson is unable to work in or have any involvement with racing, including a prohibition on entering licensed premises such as training yards or racecourses, not just in Britain but the rest of the world.
“The Panel stated in its reasons that Mr Johnson had shown a ‘reckless disregard’ for the Rules, that his behaviour ‘fell seriously short of the standard to be expected of a licensed trainer’ and that ‘any lesser penalty would undermine the confidence stakeholders in racing are entitled to hold that, reckless disregard of equine welfare, will not be tolerated.’
“This decision, and the action of the Authority in investigating this case and bringing charges, demonstrates once more that British Racing will take decisive and firm action when confronted with issues relating to welfare or integrity.”