The English Football League has said it will appeal against the sanctions imposed on Macclesfield Town in June.
The Silkmen were given a two-point deduction, which had been suspended from a previous charge, after failing to pay wages on time in March.
Macclesfield were docked 13 points in total in the 2019-20 season, which was curtailed early after a vote by clubs because of the coronavirus pandemic.
The club says it is “shocked and profoundly disappointed” at the news.
Town added they “will vigorously refute the perceived notion that the commission’s previous judgment was is in any way invalid”.
Stevenage finished bottom of League Two, a point adrift of Macclesfield.
The Hertfordshire club is set to be relegated to the National League, providing the EFL receives assurances that the top tier of non-league football will go ahead in 2020-21.
Soon after the independent panel’s decision regarding Macclesfield’s case on 19 June, Stevenage chairman Phil Wallace said his club were not ready to give up on their fight for survival.
An EFL statement on Friday said: “The EFL board has determined the League will appeal against the outcome of an independent disciplinary commission in respect of misconduct charges brought against Macclesfield Town.
“Those charges related to failing to pay a number of players on the applicable payment dates due in March 2020, failing to act with utmost good faith in respect of matters with the EFL and for breaching an order, requirement, direction or instruction of the League.
“As advised by the EFL on 19 June 2020, the commission ruled that the club was to be deducted a further two points from the 2019-20 League Two table and fined £20,000.”
In addition to those penalties, the independent panel ruled that a further four points should be deducted but suspended, and only activated if the club does not pay its players on time during next season.
The panel’s original decision stated that Macclesfield’s misconduct did “not necessitate a sporting sanction which would result in its relegation from League Two” and added that the points-per-game calculation used to decide final positions in the table had adversely affected the club, as the 13 points deducted would be equivalent to approximately 16 over a 46-game season.