The Lucknow residence of former Principal Secretary Family Welfare of Uttar Pradesh Pradeep Shukla was among the places being searched by the agency, CBI sources said.
Besides Lucknow, the search operation was going on at many other cities including Kanpur, Ghaziabad and Noida.
The sources said residences of some bureaucrats, traders and politicians are also covered in the operation.
Shukla, who was Principal Secretary during the tenure of former minister Babu Singh Kushwaha, has been questioned twice in connection with the case.
The CBI had on January 2 registered five cases against certain government and private sector officials, including one against Kushwaha alleging loss of about Rs 28 crore in implementing the centrally-sponsored scheme meant for 72 districts of Uttar Pradesh.
NRHM funds to the tune of about Rs 10,000 crore were allocated to UP for the period 2005-06 till date by the Union Health and Family Welfare Ministry.