Saints are accused of breaking two regulations:
EFL Regulation 3.4, which requires clubs to act towards each other with the utmost good faith; and
EFL Regulation 127, which prohibits any club from observing, or attempting to observe, another club’s training session within 72 hours of a scheduled match between the two clubs.
“Under EFL regulations, Southampton would ordinarily have 14 days to respond to the charges,” the league’s statement added.
“However, given the nature of the matter, the EFL will ask the independent disciplinary commission to shorten the response period and to list a hearing at the earliest opportunity.”
Southampton said the club “acknowledges the statement issued by the EFL in relation to alleged breaches of EFL regulations”.
It added: “We can confirm that we will be fully cooperating with the league throughout this process.
“Given the ongoing nature of the matter, the club is unable to comment any further at this time.”
The first leg of their semi-final takes place at Riverside Stadium on Saturday (12:30 BST), with the return at St Mary’s on Tuesday.
The rule against spying was brought in seven years ago after Leeds United were fined £200,000 by the EFL for watching opponents train before matches.
A member of Leeds’ staff was found acting suspiciously outside Derby’s training ground before a fixture between the two sides on 10 January 2019.
Manager Marcelo Bielsa revealed he had sent a member of staff to watch training sessions of every team Leeds had played that season.
The EFL found Leeds breached rules over treating teams with “good faith”.