The case is the second recent investigation into suspected fraud and money laundering in Belgian soccer. In October, there was a wave of raids and arrests, including of two referees, soccer agents and the coach of Belgian champions Club Bruges.
Investigators carried out seven searches on Wednesday - at Mouscron, at the homes of club officials and at the headquarters of two sports associations, the federal prosecutor's office said in a statement.
No one was immediately available to comment at Mouscron, but club president Patrick Declerck told Belgian broadcaster RTBF that the club was cooperating with the investigation and that, as president, he bore ultimate responsibility.
Federal prosecutors said on Wednesday they had begun investigating in April whether the club had filed false documents to conceal the control of the club by a players' agent. Soccer regulations prohibit agents from owning clubs.
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The prosecutors said they were looking into whether these actions had allowed the club illegally to maintain its status in the top division and if offshore companies controlling the club had supported it with millions of euros of illicit funding.
Rival club KV Mechelen launched a civil action against Mouscron in June to complain about licence irregularities.
Mechelen were relegated from the top division last season, with Mouscron three points and two places above them. Mouscron are currently second from bottom in the division.
(Reporting by Philip Blenkinsop; editing by Andrew Roche)
