If the different size of a penalty which is paid by the customer under the contract is provided in the Law N 44-FL and other federal law, rules of the Law N 44-FL are applied.
As has explained the Ministry of Finance, the Law N 44-FL is special in relation to other federal laws. For example, when in the contract for delivery of gas the penalty fee raised from the customer is established, the parties have to be guided by provisions of the Law N 44-FL, but not standards of the Federal law from 3/31/1999 N 69-FL.
Document: The letter of the Ministry of Finance of the Russian Federation from 3/29/2016 N 02-02-15/17609