The Premier League has called into question the future of the Football League's new financial fair play rules, warning that as they stand they are not viable.

Judging by their annual results, around half of the teams in the Championship could face a substantial fine or a transfer embargo, having fallen foul of the FFP rules agreed by the Football League in 2012. Some clubs that have spent heavily – including Leicester City, Queens Park Rangers and Blackburn Rovers – are believed to be considering legal action, along with Wolverhampton Wanderers from League One.

By going public with his concerns and revealing that the Premier League is in talks with the Football League to agree a way of better managing the gulf between their rulebooks, Richard Scudamore, the Premier League's chief executive, could sound the death knell for the rules in their current form.

"I think the Championship clubs and the Football League themselves are taking a long hard look at what they have done with their own rules," said Scudamore. "Obviously we have some concerns but these are concerns we expressed at the time when they introduced them."

The rules were the idea of the former Football League executive chairman Greg Clarke, who remains in a nonexecutive role, and were designed to try and stop clubs gambling unsustainably on getting into the Premier League. But some of those clubs argue that given the munificence of the Premier League's parachute payments, now up to £59m over four years, it will become impossible to compete with relegated clubs and remain within guidelines. Others argue that the step down from the Premier League is too great in terms of TV income and leaves clubs unable to avoid a sizeable loss in their first year back in the Football League.

Under the Championship's rules, agreed by a majority of 21 to three following two years of detailed debate, clubs losing more than £8m can be fined or have a transfer embargo imposed. QPR could face a fine of up to £48m if they repeat their recently announced annual losses of £65m.

"We thought the transition between leagues was going to be very difficult and I think there is a mood certainly around our clubs and I think with Shaun Harvey [the Football League chief executive] and the board of the Football League to sit around in a room and see if we can actually come up with something that makes that transition a little bit more manageable," said Scudamore.

The Premier League's chief executive believes there is too much of a gap between the Football League's rules and its own recently introduced financial controls. "There needs to be some proportionate linkage because we have our rules which allow X and their rules that only allow Y and if you can't bridge that delta then it's difficult. But certainly we are in discussions with them about how we might be able to reconcile that."

He added: "Their numbers wouldn't work for us and our numbers wouldn't work for them." Asked whether it was desirable for around half of the Championship's clubs to be in breach of the Football League's rules, Scudamore said: "If that is right, as a regulator you don't want to get yourself into a position where half your clubs will breach the rules, that's really not where you want to be."

Scudamore insisted that the Premier League's own less stark financial controls, including a cap on salary increases, were having an effect. "It's too early to state formally because we don't get the first reporting period until the end of this season but taking a look at the contract profiles and what people are doing then, yes, people are respecting that," he said. "We are in the first year of three in terms of the aggregate acceptable loss but in the reports that are coming through, the clubs are trying to bring their losses down so I think we are in good shape."