Special CBI judge A K Singh remanded the IAS officer in judicial custody, rejecting the agency's plea for three more days of his custody for further interrogation.
Singh fixed May 28 as the next date of hearing.
Shukla was arrested on May 10 by the CBI for alleged bungling in upgradation of 89 district hospitals under NRHM programme causing a loss of nearly Rs 22.5 crore to the exchequer.
Shukla was held from Lucknow air port while he was going to Delhi for some treatment.
The judge today allowed Shukla to carry his medicines with him, however, said that jail doctor will examine him in jail hospital and will prescribe the medicines.
During the proceeding, the 1981-batch IAS officer from UP cadre said that he never took any decision in NRHM as the order used to come from Chief Minister's office or health minister's office.
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Shukla told the court that he was only "a link" to get the order implemented and he did nothing wrong.
He also denied the agency's charge of using Rs 63 lakh in foreign travelling, saying that he went oversees for the studies of his daughter and the total expenses were born by his wife, also an IAS officer and his brother-in-law.
Jail Superintendent Viresh Raj Sharma told PTI that jail doctor has conducted Shukla's medical examination and prescribed medicines to him.
55-year-old Shukla was named in the first case registered in NRHM scam in which it was alleged that officials of UP Health Department entered into criminal conspiracy with officers of UP Processing and Construction Cooperative Federation Ltd (PACCFED) and Directors of three private firms based at Moradabad and Gajraula (all of UP).