According to CBI sources, the seizures were made yesterday. The agency also detected 11 bank accounts of the couple.
During interrogation, Malaviya, who is a BJP leader, told officials that the cheques were meant for his father and were related to a property deal.
The two were remanded by a court in CBI custody till April one on Saturday after their arrest in the early hours.
The IRS officer of 2007 batch had allegedly demanded a bribe of Rs 25 lakh from the owner of Ramayan Constructions to correct discrepancies in the company's I-T returns.
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On a complaint from the builder, CBI laid a trap and caught a person, who works with Malaviya and had allegedly taken Rs 10 lakh from the developer as part of the bribe money from a Chartered Accountant's office in M P Nagar area.
A CBI team accompanied the person to Malaviya's residence, from where the BJP leader was apprehended. The team then questioned Rai till midnight on Friday and later put her under arrest, the sources said.