The club were found guilty of exceeding the league's £1.825m cap in 2014 and 2015.
An independent tribunal concluded that a breach of the rules had been made in relation to contracts involving three players.
As well as a deduction, which puts Salford second from bottom in the table, the club were fined £5,000, but Koukash has confirmed that he will lodge an appeal.
The 57-year-old tweeted: "I owe it to the current squad and to our fans to fight the decision made by the RFL tribunal. The club will appeal."
Salford have won two of their last six games.