UKIP said the broadcaster had not invited the party to take part in a live clash to be shown on BBC1 two days before the 23 June vote.
Instead, it is believed that a senior Tory, possibly Boris Johnson or Michael Gove, will line up against a Labour figure.
A BBC spokeswoman said that conversations are still ongoing and no final decision had yet been made.
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Even so, UKIP Chair Steve Crowther has lodged a formal complaint about the party's alleged exclusion.
On Wednesday, party leader Nigel Farage told this website, "For the BBC's main EU referendum debate not to include UKIP would be a ludicrous decision.
"As the only national pro-Brexit party and having won the European elections and secured four million votes at the general election, it would be outrageous for millions of UKIP voters to go unrepresented in the BBC's biggest referendum debate."
The televised clash will take place at Wembley Arena on 21 June. The planned format will include teams of three speakers from each side of the referendum divide address the audience and take questions.
It is expected that two speakers on each side will be politicians while the third will be from a non-political background such as a celebrity or senior business leader.
The UKIP letter said: "It is widely accepted that without UKIP there would be no referendum at all. As the only nationwide political party that advocates leaving the EU which won the national European election in 2014 and secured close to four million votes at the general election last year, and which has its own separate and substantial campaigning allowance from the Electoral Commission, we believe that UKIP has an unassailable claim to be included on the main panel in this important debate."
It goes on, "For the politicians not to include Nigel Farage, the political figure most associated with the campaign to leave the EU, leaves millions unrepresented in what is undoubtedly the BBC's biggest referendum event."
"We believe these to be far smaller in stature than the final Wembley debate and in no way comparable with it.
"UKIP and Nigel Farage must be included on the main panel of your Wembley debate, to make it in any way represent the reality of the referendum debate in the country."
Meanwhile, reduction in immigration from the EU following a vote for Brexit would not lead to any improvement in living standards for those born in the UK, according to the Centre for Economic Performance (CEP) at the London School of Economics.
It also says that cuts in EU immigration would not offset the big fall in UK living standards caused by the reduction in trade and investment that would result from Brexit.
The fifth in a series of Brexit reports - co-authored by Jonathan Wadsworth, a former member of the Home Office's Migration Advisory Committee - the study analyses the impact of EU immigration on the UK, an issue that lies at the heart of the referendum campaign.