Both of them are in Chanchalguda Central Prison in connection with cases of alleged quid-pro-quo deals.
The investigating agency, through a memo filed in the court, had contended that the judicial remand of Jagan and Vijay Sai in the same jail could hamper investigations and that they could hatch conspiracies.
Without naming any jail where either of them could be transferred, CBI requested the court that it was safe to separate them "as there was danger of their planning to influence witnesses" if accommodated under the same roof.
Vijay Sai, a close aide of Jagan and also one of his alleged business partners, was arrested by CBI on January 2, 2012 in connection with the case of alleged quid-pro-quo deals involving Jagan but was granted bail by a court.
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CBI challenged the bail and moved the Supreme Court which on May 9 cancelled Vijay Sai's bail and directed him to surrender before a lower court by June 5.
Accordingly, Vijay Sai surrendered before CBI court which sent him to judicial custody after which he was shifted to Chanchalguda jail.
Both are under judicial custody till July 1.
CBI had earlier alleged that Vijay facilitated transfer of "illegal gratification" money through various companies into Jagati Publications and other business entities of the Kadapa MP (Jagan), son of former Andhra Pradesh Chief Minister late Y S Rajasekhara Reddy.
CBI in its charge sheets filed against Jagan, Vijay Sai and other accused said that they hatched a conspiracy to defraud the government.