The FA hopes to use Brexit talks to cut the amount of non-home-grown players in top-flight squads from 17 to 13.
It says it wants the reduction in 25-man squads even if there is a longer transition period or second referendum.
The proposal was met with resistance by Premier League clubs last week.
And in a statement on Wednesday, the Premier League said it was “working with clubs to operate a world-leading player development system which delivers for England teams at every level”.
It added: “There is no evidence that stronger quotas than exist now would have a positive impact on national teams.
“We approach this matter in the interests of British football as a whole and have held positive discussions with the EFL and the Scottish Professional Football League, who both agree that Brexit should not be used to weaken playing squads in British football, nor to harm clubs’ ability to sign international players.
“The three league bodies also recognise that the development pathway for young British players needs to be further enhanced and are committed to finding ways of achieving this across all professional clubs.”
Talks are ongoing after the FA, Premier League and EFL were asked by government to come up with a joint view on post-Brexit policy.
England boss Gareth Southgate has bemoaned the lack of English players in the top flight – about 30% – despite reaching the World Cup semi-finals for the first time in 28 years.
The Premier League said its efforts were “demonstrated by the many Premier League club academy and senior players that FA coaches moulded so well into Under-17 and Under-20 World Cup winners and men’s World Cup semi-finalists”.
How might Brexit affect the Premier League?
When Brexit happens, EU players will no longer have free movement between clubs and be classed the same as non-EU players.
That means they would need to meet strict criteria – such as how many caps they have won and where their country are in Fifa’s world rankings – in order to get a work permit.
But the FA also wants to create a fully open market so that if a player from the EU or non-EU were offered a contract by a Premier League club, they would meet the required governing body endorsement.
It is hoped that approach might help during negotiations about quotas.
The existing system has been in place since 2011 and a steady increase in non-home-grown players meant Premier League squads had 260 in total at the start of the 2018-19 season – an average of 13 per squad.
At the current rate of growth, the Premier League would reach its available capacity of 340 non-home-grown players by 2030.
Research also shows 65% of the Premier League’s European players would not have qualified through the current system.
The Premier League added: “Away from playing squads, it is important to recognise the global interest in the Premier League and in our clubs when they compete in the FA and Carabao Cup competitions.
“Our competition is watched in 189 countries, 700,000 visitors to the UK per season attend a match, clubs employ 12,000 full-time staff and Premier League football generates £3.3bn per season in taxes.
“We have a positive working relationship with the FA and will continue to have constructive discussions with them, and other stakeholders.”