The seizure was made during search of Bolero in Sahebpur Kamal police station area of the district, Superintendent of Police, Harpreet Kaur said.
The unaccounted cash was kept in a box, she said.
Three persons on board the Bolero have been taken into custody and interrogated, Kaur said.
The vehicle was on its way to Begusarai from Khagaria, she added.
The Election Commission and Income Tax department officials have joined probe into the recovery of Rs 40 lakh illegal cash, she said.
