Sheikh Mohammed will place the stables of Mahmood Al Zarooni in lockdown with immediate effect after saying he was "appalled and angered" in the wake of the trainer being charged by the British Horseracing Authority following tests on 11 of his horses showing the presence of anabolic steroids.
Al Zarooni will appear before a disciplinary panel of the BHA on Thursday afternoon and could lose his licence in one of the most significant doping scandals in recent racing history.
The 37-year-old has officially been charged with rule breaches related to prohibited substances, duty to keep medication records, and conduct prejudicial to racing.
The hearing will be held at 2.30pm at BHA headquarters in London.
Samples were taken earlier this month from 45 horses trained by Al Zarooni at Moulton Paddocks Stables, Newmarket.
Subsequent analysis revealed 11 of the samples contained ethylestranol and stanozolol, which are prohibited substances.
Speaking on Godolphin’s official website, Sheikh Mohammed said: "I was appalled and angered to learn that one of our stables in Newmarket has violated Godolphin's ethical standards and the rules of British racing.
"I have been involved in British horse racing for 30 years and have deep respect for its traditions and rules.
"I built my country based on the same solid principles. There can be no excuse for any deliberate violation.
"Godolphin is fully cooperating with the British Horseracing Authority to get to the bottom of this matter and take any appropriate disciplinary action.
"I have ordered the Godolphin management to undertake an immediate review of our internal procedures and controls to ensure to prevent any reoccurrence of this type of activity in any stables of mine.
"We will be locking down the Moulton Paddocks stables with immediate effect, and I have instructed that I want a full round of blood samples, and dope testing done on every single horse on that premises.
"I can assure the racing public that no horse will run from that yard this season until I have been absolutely assured by my team that the entire yard is completely clean.
"I have worked hard to ensure that Godolphin deserves its reputation for integrity and sportsmanship, and I have reiterated to all Godolphin employees that I will not tolerate this type of behaviour."
The BHA said on Wednesday information provided by Al Zarooni to investigating officers revealed that, in addition to the 11 horses which had initially tested positive, four other horses - Comitas, Sashiko, Vacationer and Tearless - were administered one of two prohibited substances.
Those horses were under the care of the Newmarket trainer, but had not been subjected to testing.
Although Comitas, Sashiko, Vacationer and Tearless were not tested and no positive samples exist, Al Zarooni faces further charges in relation to medication records and conduct prejudicial to racing.
Al Zarooni has trained a host of big-race winners, including victory in the 1000 Guineas with Blue Bunting in 2011, since joining the Godolphin team in March 2010.
Last year he won the Ladbrokes St Leger at Doncaster last year with Encke and the richest race in the world, the Dubai World Cup, with Monterosso.
Al Zarooni said on Monday he had made a "catastrophic error" in using the banned substances, saying he did not realise he had broken the rules as the horses were not racing at that time.