Championship clubs will only be allowed to spend what they earn from the 2012/13 season while sides in League One and Two will not be permitted to spend more than 55% of their turnover on player wages. Clubs who transgress the rules are likely to be handed a transfer ban as a first sanction with possible points deductions for major offenders.
Clarke said: "This could be a seminal event that reshapes football finances in England. The clubs are aware of the ground-breaking decision they have taken and we will work hard now to make it happen."
Increasing levels of debt and a drop in television income has seen the 72 clubs agree to the system "in principle" at the league's annual meeting in Cyprus, following a presentation by Andrea Traverso, UEFA's head of club licensing and financial fair play.
League One clubs also agreed to introduce a 'salary cap' from the start of the coming season where teams will only be allowed to spend a fixed proportion of their total turnover on player wages.
The system, called the Salary Cost Management Protocol (SCMP), currently operates in League Two at a 60% threshold, and this will be reduced to 55% next season. The Football League's decision means almost all teams in the four divisions will be covered by spending constraints.
Although the Premier League have not adopted the measures, 19 of the 20 top-flight clubs - all apart from Blackpool - applied for a UEFA licence last season and so would have to pass the financial fair play criteria. The Football League's move reflects concern over income - their new £195million domestic TV deal is a 26% drop on the previous one.
Debt in Football League clubs now totals £700million and a report this week by analysts Deloitte found that more than one third of clubs are paying out more in wages than they received in revenue.
Clarke added: "This is a very important step forward for professional football as it will help our clubs exert greater control over their finances.
"Much more work needs to be done, but I am hugely encouraged and impressed by the energy and focus of our clubs on this issue. They have been the catalyst for change and have shown a real desire to self-regulate in this area. I congratulate them on taking this bold step."
Source: PA
Source: PA