The LMA added: "The decision does not sit comfortably with those managers who were told that if they did not achieve Pro Licence status prior to the 2003-04 season, they would not be allowed to manage in the Premiership.
"They as a result applied themselves, in many cases at their own considerable expense, to obtain the required qualification."
The LMA were also critical of the decision to allow Glenn Roeder to continue as Newcastle manager towards the end of last season because he did not have a Uefa Pro License.
In Southgate's and Roeder's cases, both managers had stated that they were working towards achieving the necessary qualifications.