The ban on the Dubai ruler came as a result of his horse Tahhan testing positive in two two-star races for a hypertension drug and the steroid stanozolol.
Sheikh Mohammed was also ordered to pay 4500 Swiss francs in fines and legal costs.
His trainer, Abdullah bin Huzaim, who admitted giving the horse drugs before the desert races at Bahrain and Dubai, was handed a one-year ban.
Under FEI rules, the person riding the horse in an event is responsible for any drug breaches, although other support personnel may also be held accountable if circumstances dictate.
The FEI tribunal, comprising Patrick Boelens, Philip O'Connor and Erik Elstad, said in its decision that Tahhan competed in a 120km race in Sakhir, Bahrain, on January 10 this year and a 120km race in Dubai on February 28, in both cases ridden by the sheikh.
The horse was selected on both occasions for blood testing, and was also routinely tested at his home stable, when the positive tests were returned.
One of the prohibited drugs detected, Guanabenz, is used to treat blood pressure in humans and is known to have a calming and painkilling effects.
The other drug, Hydroxy-Stanozolol, is a metabolite of Stanozolol, which is an anabolic steroid.
The sheikh was advised and, through his counsel, Rachel D.S. Hood, said he would cooperate with the FEI in every way possible and provide additional information as it became available.
On April 6 the sheikh was advised he was provisionally suspended and was granted the opportunity to be heard at a preliminary hearing before the FEI Tribunal. He did not request a preliminary hearing and declined to exercise his right to have the B-Sample tested.
On April 21, the sheikh submitted a written explanation.
"In a nutshell," the tribunal wrote, "the person responsible submits that he is an amateur rider competing for several stables and that he is typically presented with a choice of which horse to ride on the day of a race.
"[He] submits that he has an interest in some 700 horses in the field of endurance racing and that he cannot be involved in the medication protocols of each horse.
"Therefore he contends it is reasonable for the person responsible to rely upon the stables, the trainer and the veterinarians to present horses that are fit to ride and which are not in breach of ... applicable rules and regulations of the FEI.
"Further, that it was contrary to routine practice in the UAE, particularly for amateur riders, to involve themselves in, or make specific enquiry into the horse's medication, which are matters customarily dealt with by trainers and veterinarians."
In both cases, the sheikh said he had been presented with the horse only some minutes before the race commenced. He had enquired as to whether all was well with the horse, and was assured that all was in order.
He said that following the positive samples he promptly initiated his own inquiries as to how the prohibited substances could have entered into the horse's system.
"Referring to the statement of the trainer, Mr Abdullah bin Huzaim, the person responsible submits that Mr Abdullah bin Huzaim caused the prohibited substances to be administered without his knowledge, and that if he had had such knowledge, he would not have ridden the horse."
The tribunal referred to the statement of Abdullah bin Huzaim, who admitted that the respective substances had been administered without the knowledge of the sheikh before the two events by the veterinarian, under his direction.
"Mr Abdullah bin Huzaim stated that he 'believed that the horse required those medications' and that he believed that they would 'both be outside FEI detection times'."
In later submissions, the sheikh indicated that while his stables are first class and properly managed, with all of the appropriate controls in effect, a detailed enquiry into security management had been implemented following the positive sample results to see whether stable management could be improved.
The tribunal found the charges proven.
"The person responsible has an obligation to ensure that all precautions are taken to be certain that his horse participates in international competitions without prohibited substances in its system, which was undoubtedly not what happened in the present case.
"No evidence was submitted indicating that the person responsible had given strict written or other instructions to the stable staff to ensure that no prohibited substances were administered to any horse that was likely to compete in international competitions.
"The tribunal has repeatedly expressed the view that it is the responsibility of competitors to inform themselves of all substances administered to horses which are destined for participation in international events and to ensure that such horses do not have any prohibited substances in their systems.
"Generally, therefore, the tribunal is of the opinion that competitors are responsible for what their staff provides to the horses and whatever treatments it administers to them. However, the tribunal also recognises that the application of this rule can be different when it comes to persons responsible with high social and governmental status.
"While the Tribunal would not expect the person responsible in this case to be personally working in the stables, the tribunal does expect him to take a senior level of responsibility to enforce stable management that demonstrates respect for the applicable rules and horse welfare.
"Put more simply, as a person of high government status executes his governmental role from a position of authority and effective delegation, the same principle should apply to stable management.
"Further, the tribunal would expect evidence of excellent stable management to be submitted in such cases so that the tribunal can be comforted that the stables are being properly and effectively supervised so as to ensure a high likelihood of compliance with FEI Rules.
"No such evidence was submitted in this case.
"Accordingly, the tribunal finds that the person responsible has acted negligently in performing his duties as competitor and person responsible, given that a trainer was permitted to cause the administration of prohibited substances without his knowledge."
It continued: "The strict responsibility of the person responsible is necessary in the fight against doping and to protect the principles of fair play and promotion of equal conditions in the conduct of international events, as well as with regard to horse welfare.
"Nevertheless the tribunal appreciates the fact that the person responsible co-operated with the FEI and initiated an investigation which revealed that the trainer had caused the administration of the prohibited substances to the horse."
In deciding on the sanctions in the case, the FEI Tribunal took into account the type of substances involved and the fact they were deliberately administered to the horse, as well as the rider's "amateur status", and the fact he had proactively informed the FEI of the positive test results.
The FEI said that under the rules disqualification is automatic when there is a positive finding. It also found that the trainer had deliberately administered the substances, and stated that even so he miscalculated the withdrawal time of the substances, he "clearly [...] wanted His Highness to do well with the Horse".
"This behaviour is not acceptable and needs to be sanctioned severely," the FEI said.
Sheikh Mohammed was suspended for six months starting from April 3, the date of the initial notification. He was fined 3000 Swiss francs and ordered to contribute CHF1500 towards legal costs. The trainer, Abdullah bin Huzaim, was suspended for 12 months, also from April 3. He was also fined CHF4000 and ordered to contribute CHF1500 towards legal costs.