Boro staff reportedly confronted the individual for taking photos and videos, but he allegedly refused to cooperate and fled into another area of the training complex.
"Southampton Football Club has today been charged with a breach of EFL Regulations, and the matter will be referred to an Independent Disciplinary Commission,” a statement from EFL read.
"This follows a request from the EFL for the club’s observations after a complaint from Middlesbrough relating to alleged unauthorised filming on private property ahead of the two clubs meeting in Saturday’s Sky Bet Championship Play-Off semi-final first leg.
"Under EFL Regulations, Southampton would ordinarily have 14 days to respond to the charges. 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."
EFL regulations strictly ban clubs from spying on opponents’ training sessions within 72 hours of kick-off, a rule introduced after the 2019 “Spygate” controversy.
Middlesbrough will host the Saints in the first leg of their Championship play-off semi-final at the Riverside Stadium on Saturday afternoon.