A Rugby Football League statement said the alleged breaches concern "contractual arrangements made with Salford players in 2014 and 2015".
No date has been set for a hearing.
If Salford are found to have exceeded the £1.825m wage ceiling in the last two years and are docked 20 points, it would wreck their season when it has started with some promising displays.
However Wigan, the last club to be found in breach of the salary cap in 2007, were only docked four points.
The Red Devils, coached by Ian Watson, lie sixth in the table after collecting four points from their opening five games.
Their points tally would have been higher had it not been for last-minute defeats by Wigan and Warrington.
The RFL's announcement comes six weeks after Bradford chairman Marc Green raised questions over Salford's use of the cap over the last two years and in particular their signing of Tony Puletua from St Helens in 2014.
Green claimed he was prevented from raising his concerns at a RFL Council meeting in December and called on the governing body to fully investigate the transfer of Puletua.
Salford have yet to comment on Thursday's news although owner Marwan Koukash tweeted: "I do not know what all this fuss is about. Calm down!"
In January Koukash said his club had been fully co-operating with the RFL investigators since early October.
Salford could be docked as many as 20 points after being charged with salary cap breaches.