The British Horseracing Authority (BHA) banned Zarooni for eight years after finding him guilty of administering anabolic steroids at his stables in Newmarket last year.
"I was shocked, really," Godolphin owner Sheikh Mohammed, who is also Prime Minister of the United Arab Emirates, told the BBC on Sunday.
"I have many trainers and if one of them does the wrong things, you know - they gave him eight years, and I gave him lifetime. Finished," he said.
"He comes and sees some other friends but he will never come near horses."
The BHA said in July the scandal, which caused serious embarrassment to Sheikh Mohammed, was a result of Zarooni acting alone without knowledge of his senior staff.
Zarooni, who won the Dubai World Cup - the world's richest horse race for Godolphin in 2012 - with Monterosso, as well as English Classics the St Leger and 1,000 Guineas, admitted administering prohibited substances to horses at the Moulton Paddocks stable.
Sheikh Mohammed closed the stable and ordered internal investigations. Assistant trainer Charlie Appleby was later put in charge of some 200 horses that were in Zarooni's care.
In September, Princess Haya, who is also a president of the International Equestrian Federation (FEI), appointed former London police chief Lord Stevens to oversee an internal inquiry into the sheikh's global equine interests.
Asked how horses could have been doped without the his knowledge when he is famed for his attention to details, Sheikh Mohammed said: "He (Zarooni) doped them not for racing, but for treatment long term."
"Now Lord Stevens will find out the whole story and we will all know what happened. He hasn't finished yet but I hope good luck for him. The truth will come out because of independent Lord Stevens," he said.
In May, Sheikh Mohammed said imports, sale, purchase and giving anabolic steroids to horses will become a criminal offence in the UAE, which has seen a number of doping cases in popular long-distance horse endurance races.
Godolphin, which takes its name from The Godolphin Arabian, one of the three foundation stallions imported into England nearly 300 years ago, have won 209 Group One races in different countries since Sheikh Mohammed established training operations in Dubai and England in 1992.
(Reporting by Martin Dokoupil; Editing by Amlan Chakraborty)
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