The fund over Rs 95,000 crore came to Bihar under Mahatma National Rural Employment Guarantee Act (MNREGA) and other flagship programmes for the poor people.
"The NDA government will not succeed in either influencing or creating obstacles in the way of the CBI investigation into the alleged misappropriation of the central funds," said Pilot.
The state government had spent a huge amount of money publicity for the assembly polls 2010.
Patna High Court had ordered a CBI probe into misappropriation and illegal withdrawal of Rs 11,412 crore from state treasury by the state governments since 2002.
Pilot demanded a speedy investigation by the central agency to bring the culprits as soon as possible.