The HMRC said at the time that French authorities were assisting their efforts and searches had been carried out in France in connection with the investigation, which centres around transfer dealings between English and French clubs.
Newcastle challenged the legality of the HMRC's search-and-seize orders, but the presiding judges at a hearing at Leeds Crown Court ruled on Wednesday that "the warrants were lawfully issued".
The HMRC weclomed the decision and said it was proceeding with its investigation into suspected tax fraud.
"HMRC is pleased that the Court agreed these warrants were lawful and justified in this case, and rejected each of the five grounds for which the review was sought," a spokesperson said.
A Newcastle spokeswoman said in a statement that the north-east club were deciding whether to appeal.
"We are disappointed with this decision given the Court's findings," she said. "We are considering all of our options with our advisers, including whether to pursue an appeal."
Newcastle were promoted to the Premier League in May.
(Reporting by Shrivathsa Sridhar in Bengaluru; editing by Ken Ferris)
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