Last year's Ladbrokes St Leger hero Encke was the highest-profile name among seven further Mahmood Al Zarooni-trained horses to test positive for anabolic steroids.
Following the former Godolphin trainer's eight-year ban for administering banned drugs to 15 horses in his care, the British Horseracing Authority tested every inmate at his Moulton Paddocks yard in Newmarket.
Those checks produced positive tests for another seven horses, including the Doncaster winner, with the steroid stanozolol found to be in their blood samples.
Testing at the other Godolphin yard of Saeed bin Suroor returned no positive results for banned substances, the BHA said.
Encke will now be suspended from running for six months, meaning he cannot return to action until October 29, when only a few weeks of the Flat season remain.
The other six horses - Energizer, Genius Beast, Improvisation, Stamford, Steeler and Zip Top - will also be barred from racing until that date.
Encke made great strides in 2012, graduating from a Sandown handicap via Group-race places at Goodwood and York to foil the Triple Crown bid of Camelot.
In beating Aidan O'Brien's charge by three-quarters of a length, Encke ended Camelot's chances of emulating Nijinsky, who was the winner of the 2000 Guineas, Derby and Leger in 1970.
The BHA said Encke was routinely tested after finishing third in the Great Voltigeur at York and after his Doncaster triumph, with the colt returning negative results on both occasions.
Given his negative post-race test last September, the BHA said it was satisfied Encke was clear of any banned substances when landing his Classic success and would not be disqualified.
Al Zarooni has lodged an appeal against the severity of his initial suspension and the BHA has confirmed it will not take any further action until that matter is resolved, with the last week in June currently mooted as a potential hearing date.
Adam Brickell, director of integrity, legal and risk for the BHA, said: "We will not be taking any separate action in respect of these additional positive results whilst Mr Al Zarooni's appeal process is on-going.
"In the meantime, the latest findings from HFL Sport Science will form the subject of further interviews as part of the BHA's continuing investigation.
"From the outset, one of the aims of the investigation, in addition to trying to understand the environment within which such serious breaches came to be committed, has been to identify what measures are needed to ensure the yard operates in accordance with the Rules in future.
"The findings will be shared with Godolphin and will also assist the BHA with regard to the future licensing of the yard."
Paul Bittar, the BHA chief executive, said: "These test results endorse the swift action and measures taken by the BHA in this matter.
"Whatever the outcome of his appeal before the independent Appeal Board, the gravity and scale of the infringements warranted Mahmood Al Zarooni being removed from control of the yard as quickly as possible.
"We welcome the news that Saeed bin Suroor's horses tested negative and this clears the way for him to now take charge of Moulton Paddocks."
Godolphin founder Sheikh Mohammed locked down Al Zarooni's stable after the initial positive tests were announced, a measure racing manager Simon Crisford believes was fully justified following the "disappointing" news of further cases.
"It is obviously very disappointing that seven further horses have tested positive for stanozolol," he told www.godolphin.com.
"These results highlight why H.H. Sheikh Mohammed took the decision to lock down the stables at Moulton Paddocks until every Godolphin horse in training at Newmarket had been tested.
"All of Saeed bin Suroor's horses have tested clear and we are working with the BHA to put everything back in order at Moulton Paddocks."
Bin Suroor, who won the Group One JLT Lockinge Stakes at Newbury on Saturday with Farhh, will now assume temporary control of Al Zarooni's former yard while Godolphin seek a new trainer.
He said: "I'm happy that my stable is clear. I said before, the BHA can come any time they like, I've got absolutely nothing to hide.
"Ever since we started, everything has gone in the books. I knew 100% that they wouldn't find anything and now everybody else knows the same.
"It will be very busy (running both yards) but it will only be temporary. It will be just for a few weeks until we get somebody else in."
Energizer was previously a Group Three winner at Royal Ascot when trained in Germany, while Steeler won the Royal Lodge last year for Mark Johnston and had featured in the Investec Derby betting.