Rejecting the bail pleas, special judge S Lal sent Shukla and UP Project Corporation Ltd employees Devendra Mohan and Ravendra Rai to judicial custody till May 22.
The three accused had appeared in the court where their counsels sought regular bail for them, prosecution counsel B K Singh said.
After hearing both the prosecution and defence counsels, the judge sent the trio to judicial custody.
CBI has filed two cases against Shukla, the then family welfare secretary. The suspended IAS officer and former family welfare minister Babu Singh Kushwaha are named as accused in one case in which he got bail on August 9 last year.