Special CBI Judge A K Singh granted him bail on a personal bond of Rs five lakh and two sureties of five lakh each.
CBI sources said the agency did not file the chargesheet against him because the Centre did not accord sanction for his prosecution.
They said the agency has sought permission to prosecute the 1981-batch IAS officer of UP cadre in connection with alleged irregularities in implementation of NRHM scam about a month back.
But despite the gravity of charges against him, the Department of Personnel and Training did not give the necessary sanction, they said.
In the absence of sanction for prosecution, CBI could not proceed with the filing of the chargesheet, they said.
Known as powerful bureaucrat in the state, Shukla was arrested by the agency on May 10 this year.
According to rules, CBI had to file a chargesheet within 90 days of his arrest to keep him in judicial custody.
Shukla had held the charge of Principal Secretary Health and Family Welfare during 2009-11 when the alleged scam took place.
The agency has booked Shukla in three separate cases of alleged irregularities in January this year.
The total cost of the projects in which these three cases have been registered is over Rs 250 crore and mainly deal with the construction and upgradation works in hospitals across Uttar Pradesh.
Former UP minister Babu Singh Kushwaha, who is already lodged in jail for his alleged involvement in the scam, has levelled allegations against Shukla for being among the officials who signed the papers for fictitious payments.
Ghaziabad: Senior bureaucrat Pradeep Shukla, an accused in National Rural Health Mission scam in Uttar Pradesh, was today given bail by a special CBI court here when the agency failed to file its chargesheet against him within the stipulated time of 90 days.
First Published: Wednesday, August 08, 2012, 23:05