The CBI special judge S Lal issued the warrant against Shukla for not appearing in the court in its last hearing, officials said.
The court has fixed January 31 as the next date of hearing in the case.
The agency had filed chargesheet against Shukla last month for his alleged involvement in the irregularities in upgrading of 89 district hospitals in the state, under National Rural Health Mission scheme, causing a loss of Rs 16 crore to the exchequer.
Shukla and officials of UP Processing and Construction Cooperative Federation Ltd (PACCFED), including its managing director V K Chowdhary, the then DG of family welfare S P Ram, Moradabad-based businessman Saurabh Jain, and his firms were booked by the CBI in January last year.
The 55-year-old UP-cadre IAS officer, serving as member revenue board, was arrested by the agency in May but was released on bail.
After release, Shukla joined back as member of revenue board but the UP government issued orders of him being "deemed suspended".
CBI alleged officials of PACCFED favoured ineligible firms and released payment of Rs 16.93 crore on the basis of forged documents.
In its chargesheet, the agency alleged Shukla along with Ram entered in criminal conspiracy with private firms and gave contract related to upgrading of district hospitals in Uttar Pradesh worth Rs 89 crore on the basis of forged documents.
