Besides Uttar Pradesh, the searches were being carried out at other places including Delhi and Haryana.
Official sources said the cases were registered on January two in a designated court at Lucknow after which CBI sought search warrants against the accused people.
The searches began this morning at 60 places including at the residence of the former Minister, who joined BJP yesterday after being sacked by UP Chief Minister Mayawati.
The CBI had filed FIRs pertaining to the scam. Kushwaha has been named as an accused in one of the five FIRs registered against the NRHM officials and private companies in UP.