Godolphin racing manager Simon Crisford "deeply regrets" the part he played in hiring Mahmood Al Zarooni.
Crisford recommended Al Zarooni to Sheikh Mohammed but believes he showed a "remarkable lack of judgement" after the trainer was banned for eight years for administering anabolic steroids to 15 of his horses.
Two of Al Zarooni's horses failed tests for painkillers last April, after which Crisford stressed to him the importance of keeping his medical records up to date.
"I think we have to be very clear about this situation," Crisford told Channel 4 Racing. "A trainer is a licensed individual and it is his duty to take professional care of the horses in his stable.
"He runs the day-to-day management, my job is to look after the best interests of the owner. I simply cannot be aware of every single bit of medication that every horse in Godolphin is getting.
"Saeed bin Suroor and Mahmood Al Zarooni are supposed to be professional trainers. One of them clearly wasn't.
"It's deeply regrettable (that we hired him) and shows a remarkable lack of judgement on my part to recommend him to Sheikh Mohammed, which I did do.
"When his horses failed the tests for painkillers last year, we sat down with him and told him he had to keep his records maintained in a much more efficient manner.
"I had lengthy conversations with him about that but I'm afraid he's betrayed the trust we put in him and he's let everybody down, not only Godolphin but the British public, too. We'll have nothing to do with him again and I have no sympathy for him.
"It will take a long time to recover from this, but Sheikh Mohammed will make sure everything is done and that the stable is 100% clean before any horses get transferred to any other stables."
British Horseracing Authority chief executive Paul Bittar stressed the investigation is not yet complete and further charges could be brought against the other individuals that were involved.
He said: "Rarely do we have a situation where the trainer puts up his hands and gives us a list of everybody else that has been involved in the giving of the medication. Ultimately we were able to deal with it quickly because of the public interest issue.
"We certainly didn't do this on Godolphin's terms but rarely to you get their level of cooperation.
"There have been some suggestions that Al Zarooni wasn't even in the country when the steroids were administered but the evidence we have - written evidence from Godolphin and Al Zarooni - suggests that he was A, in the country, and B, he was responsible for directing the administration of the drugs.
"Some of the investigations are on-going. The vet's assistant who has been mentioned is a nebulous term in a way as he's not really a vet at all, he just simply assists but he's not captured under the rules.
"The interviews with the foremen are on-going and that part of the investigation is on-going but because of Al Zarooni having responsibility for the horses we needed to deal with him first.
"We asked Al Zarooni if he'd ever administered steroids before and he said he hasn't. Both his yard and Saeed bin Suroor's have been tested before and all those results came back negative.
"The investigation is not complete and whether the evidence brings about further charges I couldn't comment, it's wherever the evidence takes us."