Government contractor. Can government stop our payments for work done?

We are turnkey contractors for electrification work. We have been working for the Government for quite some time now. So while executing our work this time, we had raised the bill for the entire supply of the material at the beginning and now the project is nearing its completion and we have supplied the entire material and erected most of it.

But due to some officials an enquiry is being conducted and the government has stopped all our payments. Kindly guide me as on what can the government do if the enquiry report goes against us.