Godolphin's plans for Saeed bin Suroor to take charge of the Newmarket stables previously run by the banned Mahmood Al Zarooni have been blocked.
The British Horseracing Authority (BHA) says it will not grant a licence for Bin Suroor to take over until the results of drug tests on all the horses trained by Al Zarooni are known.
Al Zarooni is currently
appealing against his eight-year doping ban.
Bin Suroor also trains for Godolphin at its Snailwell Road stables.
Godolphin had hoped the switch, described as temporary until a permanent replacement is found, would be a formality.
The BHA expects to receive the results of the tests, which were ordered after 15 horses were administered outlawed anabolic steroids on Al Zarooni's orders, next week.
Before the BHA blocked the decision on Thursday, Godolphin had announced that Bin Suroor would be taking over the training licence at Moulton Paddocks on a temporary basis until a new trainer was appointed.
"The role is in addition to Saeed bin Suroor's responsibilities for horses based at Godolphin Stables in Newmarket," said Godolphin.
The 15 Moulton Paddocks horses that were given anabolic steroids, including one-time 1,000 Guineas favourite Certify, have been banned from running for six months.
Bin Suroor, 46, is Godolphin's longest-serving trainer, having joined the operation in 1995, and has won the British trainers' championship on four occasions.
The Godolphin operation is run by the ruler of Dubai, Sheikh Mohammed bin Rashid Al Maktoum.