It may not be possible to give an accurate advice on facts since detailed examination of records is necessary for this purpose. But, from what you have written, it appears that the contractor has already done the work. If there is no defect in work and if the work is satisfactory, then, generally speaking, payment may have to be made to him. If he has violated the rules by doing work in more than one districts, then perhaps, it would have been advisable to not give any work to him in the first instance, since you have mentioned that he is blacklisted. The general principles of law of equity would require that the work done should be paid for. However, it is for the court to take a call and decide the issue on detailed consideration of all facts, including whether the fraud perpetrated by him goes to the root of the issue so as to deny him even the payment for the work done by him. At the same time, even if you have made payment to him, you can separately consider whether it would be possible for you to take some civil action against him for violation of the terms of the agreement.
You, being in Government, should be in a position to consult some good Government lawyer by showing him full details of the case.
Dr. Ashok Dhamija is a New Delhi based Supreme Court Advocate and author of law books. Read more about him by clicking here. List of his Forum Replies. List of his other articles. List of his Quora Answers. List of his YouTube Videos.