The 2012 St Leger winner Encke is among seven horses to test positive for anabolic steroids as the investigation widened into doping involving Sheikh Mohammed's Godolphin operation.
The British Horseracing Authority (BHA) revealed on Monday it had undertaken an extensive testing program at the yard of former Godolphin trainer Mahmood Al Zarooni following his recent eight-year suspension for administering banned drugs to 15 horses in his care.
The latest BHA testing returned positive results for the steroid stanozolol and Encke will now be banned from racing for six months, meaning he cannot return to action until October 29.
Encke won the Doncaster classic last September at long odds, in the process upsetting the 2000 Guineas and Derby winner Camelot's Triple Crown bid.
The other six horses - Energizer, Genius Beast, Improvisation, Stamford, Steeler and Zip Top - will also be barred for six months.
Testing at the other Godolphin yard of Saeed bin Suroor returned no positive results for banned substances.
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 favoured as a potential hearing date.
"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," the BHA's director of integrity Adam Brickell said.
"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."