The Protocol is part of the Brexit divorce deal aimed at avoiding a hard border between Ireland and Northern Ireland. Under the terms of the deal, Northern Ireland effectively remains in the EU single market following the end of the transition period meaning checks take place on goods arriving from mainland Britain.
The UK Government has said they could take what is seen to be the "nuclear option" of triggering Article 16 of the protocol to effectively tear up parts of the deal if no movement is made on British demands for the European Court of Justice to be removed from oversight in Northern Ireland.
White House insiders said on Tuesday night that Mr Biden asked his staff for an update on the negotiations between both sides.
A senior source added President Biden had asked a message to be relayed to Downing Street to say Ministers “should not do anything that could jeopardize the 1998 Good Friday Agreement”.
President Biden argues the Protocol protects the 1998 peace deal, agreed after The Troubles.
Mr Biden’s calls echo a meeting the US President had with Prime Minister Boris Johnson last month where he stressed the importance of protecting the peace deal.
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