The 28-nation bloc was upgraded from an international organisation to a member state in 2016, under former president Barack Obama.
Without announcing the move, German broadcaster Deutsche Welle reported that its status had been relegated to its previous position.
This only came to the attention of EU officials when the ambassador to Washington, David O'Sullivan, remained uninvited to certain events last year.
“We don't exactly know when they did it, because they conveniently forgot to notify us," an EU official told the broadcaster. "I can confirm that this has not been well received in Brussels.”
EU diplomats were given final confirmation when Mr O’Sullivan was “called up as the last person” invited to former president George HW Bush’s funeral last month.
The State Department traditionally calls ambassadors to high-profile events in chronological order – from longest-serving to newest.
As one of the longer-serving diplomats in Washington, Mr O’Sullivan would have expected to have been among the first to receive an invite.
Officials believe the downgrade likely occurred in October or November.
The move by the Trump administration effectively repeals the change in status made in the last day's of Mr Obama's presidency.
It is likely to raise further suspicions among European diplomats over increased hostility by the US government under Mr Trump towards Brussels.
A spokesperson for the EU, Maja Kocijancic, said: "We understand that there was a recent change in the way the diplomatic precedence list is implemented by the United States’ Protocol.
"We are discussing with the relevant services in the administration possible implications for the EU Delegation in Washington.
"We were not notified of any change."
The State Department said it could not comment due to the US government shutdown imposed by Mr Trump.
"Due to the lapse in appropriations, the Press Office will be operating on a reduced status," it said in an email.
"Communications with the media will be limited to events and issues involving the safety of human life or the protection of property, or those determined to be essential to national security."
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