Luton and six agents were accused of breaking rules in a number of transfer and contract negotiations.
Luton is also accused of making payments totaling about 160,000 pounds (US$327,332; 223,737 EUR) to six licensed agents through its holding company, Jayten Stadium Limited, rather than through the club as FA rules require.
The FA said the six licensed agents - Sky Andrew, Mike Berry, Mark Curtis, Stephen Denos, David Manasseh and Andrew Mills - did not enter into proper contracts with the club during negotiations and knowingly accepted payment from the wrong source.
Andrew said that any offense he had committed was at most a "technical breach" and was a "paperwork" issue.
"Me, myself and my company adhere to every rule in the game," he said.
The FA has charged former Luton chairman Bill Tomlins and former finance director Derek Peter over the payments, and current directors John Mitchell and Richard Bagehot for not alerting the FA when they found out about them.
Tomlins resigned in April after admitting to making three irregular payments to agents.
Luton said in a statement that it acknowledged the charges but had no comment to make at present.
Those accused have until Nov. 30 to respond to the charges.
In January 2006, former Luton manager Mike Newell claimed he had turned down two bribes offered by agents to complete player transfers.