Bowyer will miss the next six European games
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An administrative error means Lee Bowyer has yet to serve his six-game ban from European competition.
Newcastle thought Bowyer would be available to play in their Uefa Cup tie against Valenrenga on Thursday.
But he was not registered as "eligible to play" in their six European games this season, so has not served the ban.
United argue they are not at fault, saying they checked with Uefa and the FA, but Uefa said on Tuesday the club failed to understand its rules.
"For a player to serve his ban, he needs to first be listed as an eligible player. This is nothing new," a Uefa spokesman said.
In a statement, Newcastle claim they were "shocked and exasperated" to hear of the ruling, which was made by Uefa's control and disciplinary body.
The decision was upheld in December by Uefa's internal appeals court after an appeal by United and the FA.
Newcastle's only remaining option is to pursue the matter with the Court of Arbitration for Sport in Lausanne - but they admit they are unlikely to do so.
"Despite willing support, the club is extremely annoyed with the FA and extremely disappointed by
Uefa's decision," said the statement.
"(The club) expected fair play and a common-sense approach, but now further appeal appears futile.
"The club still maintain and believe the player, who has done nothing wrong, is being particularly unfairly treated - his ban has been effectively doubled."
The FA insisted it acted as soon as Newcastle brought the matter to light, and revealed that it was unhappy with Uefa's ruling.
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The FA believes that the rules on eligibility are ambiguous
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A statement from the FA said: "The FA was first asked by Newcastle United to clarify the situation with Lee Bowyer in October 2003.
"The FA immediately contacted Uefa to seek clarification of Bowyer's status, as happens on a regular basis concerning players with English clubs competing in
Europe.
"Given the wording of Uefa's competition regulations, the FA was equally surprised at Uefa's interpretation of the situation and therefore gave its full support to Newcastle United's appeal, including making representations at Uefa headquarters in Nyon.
"The FA believes that the rules on eligibility are ambiguous and should not be open to differing interpretations, and are continuing to make this position
clear to Uefa."
So far this season the Magpies have played two Champions League qualifying matches - losing to Partizan Belgrade on penalties - and four Uefa Cup games, reaching the third round of the competition.