The Teesta river catchment is also expected to receive heavy rains.
The department had yesterday issued warning of "very heavy rainfall" in Bihar and Jharkhand.
As cyclonic storm Phailin moves ahead, the sub-Himalayan region in Nepal are expected to receive "very heavy rainfall" over the next 48 hours.
Due to this, the catchment areas of Kosi and Gandak rivers are also expected to receive heavy rainfall. This could lead to flood like situation in Bihar.
"Phailin has weakened considerably and by the time it reaches the sub-Himalayan region it will be a low pressure area. However, it still has clouds that could potentially lead to very heavy rainfall," the official said.