Ministers are battling to stop Brexit bringing an added layer of bureaucratic chaos to one of football’s most frantic periods – the January transfer window. A summit held last week between the Home Office and football authorities saw ministers attempt to prevent confusion over the post-Brexit immigration system scuppering new signings.

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The new immigration regime is set to be rolled out from January 2021, at the end of the transition period that would come as part of the Brexit deal on offer from the EU. However, January also marks the mid-season transfer window, when clubs desperately attempt to secure last-minute deals to bolster their squads.

There are concerns in Whitehall that some clubs are not alive to the changes, which will mean European players lose the automatic right to come and play for British sides.

The summit came during a remarkable week of footballing success for English clubs, which saw Liverpool and Tottenham fight back to claim their places in the Champions League final. Arsenal and Chelsea also ensured that the Europa League final would be contested by English sides. Of the 12 goals scored by the four clubs in their European clashes last week, 11 came from overseas players.

Gareth Southgate, the England manager, was among those at last week’s gathering and is understood to have been keen to use Brexit as an opportunity to boost the number of homegrown players in top teams. Caroline Nokes, the immigration minister, and Martin Glenn, the Football Association’s chief executive, were also at the meeting.

The January transfer window is already notoriously chaotic, with managers, owners and agents all working up until the deadline to secure players and sign contracts. A new immigration system risks adding complications. Home Office officials are attempting to work with the football authorities to ensure everyone is aware of the new visa regime when it comes into force.

Under current rules, all players from EU nations are free to come and play for English clubs under the EU’s free movement rules. Those rules will cease to apply once Britain leaves the bloc and the Brexit transition period has ended, with clubs having to secure visas for their new stars.

To secure a visa, non-EU players have to apply for a Governing Body Endorsement from the FA. It can be secured once they have a club to act as a sponsor. Their eligibility depends on a series of factors, including the number of appearances they have at international level and the ranking of their national team.

Meanwhile, the FA is understood to have used last week’s meeting to outline the opportunities for homegrown talent that could be created after Brexit. It has backed a plan to increase the minimum number of home players in each squad from eight to 12.

Southgate has previously complained about the falling numbers of English players in the top flight. During some weekends this season, fewer than a quarter of the players starting Premier League matches were eligible to play for England. The England manager warned last year that it was no longer true that English players would be given a chance at top clubs if they were good enough.

“Nobody can tell me that if players are good enough, they will come through,” he said. “That is not true. There are plenty of players who are good enough. In terms of the quotas, we are in ongoing discussions on those. What’s clear is that we can’t allow the trend to continue as it is because at what point do we stop?”

The Premier League has been opposing tightening the rules around overseas players and has said that “access to talented footballers from across Europe has played a key part in the growth of the Premier League”.

An FA spokesperson said: “We are continuing to work with the Premier League, English Football League and a range of government departments, including: DCMS; Home Office; Treasury during this consultation period.”