Macclesfield have been fined �62,000 and told to pay the Football Foundation �195,000 after an inquiry into the funding of their Estate Road Stand. The investigation centred on a payment made to the previous administration of the Moss Rose outfit in connection to the stand during 2000-02.
The club, which has the right to appeal against the punishment, says the fine threatens its existence.
Macclesfield say the blame lies with the club's former regime.
Football Foundation regulations forbid clubs to receive any more than 80% of the total funding for a construction project but it has been established the payment eventually covered the entire cost.
The charges centred around two allegations of receiving funding before and without paying contractors for the work, which is also against Football Foundation regulations and also a supposed sponsorship deal with the contractors.
The inquiry eventually heard Macclesfield supplied bogus invoices suggesting they had paid their share of the construction costs up front, when in fact no payment had been made.
In addition, rather than being an actual sponsorship deal, the contract with the constructors merely shaved some of the cost off the entire project.
This meant the Football Foundation eventually bore the whole cost of the stand, so the FA have ordered the Cheshire club to repay the overspend before 31 January next year.
"The club admitted a charge of improper conduct for receiving funding before paying contractors and another charge of improper conduct for receiving funding without paying contractors," said FA in a statement.
"They were fined �10,000 for each of these breaches.
"The club denied a charge of improper conduct in relation to sponsorship payments received from the main contractor which were alleged not to have been genuine sponsorship amounts, but rather a saving or discount against the value of the project.
"The Commission found this charge to be proven and issued a fine of �40,000.
"The club denied a separate fourth charge relating to their accounting records. The Commission found it to be proven and fined the club �2,000."