It is possible to provide in the contract that the state customer holds a penalty from a payment amount under the contract

Such line item of the Ministry of Finance was stated in the letter by the FTS. The Ministry of Finance expressed similar opinion and earlier, in November, 2015.
The ministry specified that it is possible to provide in the contract based on provisions Civil Codes of the Russian Federation the following condition. If the partner doesn't fulfill or will fulfill in an inadequate way the obligation on payment of a penalty, the customer based on requirements about payment of a penalty charges debt and pays it for the contractor in the budget. For this purpose the customer takes means from a payment amount under the contract.
Thereby payment of the contract is made by payment to the contractor of the amount reduced by penalty size.
Let's note, the similar position is taken also by FAS. According to anti-monopoly service, inclusion in the draft contract of a condition on an opportunity to pay it less a penalty doesn't contradict the Law N 44-FZ. The Ministry of Economic Development also expressed similar opinion.
Let's remind, under the Law N 44-FZ the direction to the contractor of the requirement about payment of a penalty is the customer's obligation. He will shall make it if the partner allows delay of obligation fulfillment under the contract, and also in other cases of their non-execution or improper execution.
Document: Letter of FNS of Russia of 17.02.2017 N AC-4-5/3049