Federal prosecutors said that the raid took place near the western city of Mainz. The two men are "suspected of taking part in the Syrian civil war as members of a foreign terrorist organisation," prosecutors' office spokesman Michael Neuhaus said in an email.
He declined to provide further details, including whether the men had been arrested, citing the ongoing investigation.
News website Spiegel Online reported that it had tracked down one of the men - a 32-year-old suspected former commander in the Islamic State group - before the raid in Sankt Johann, a town about 20 kilometres south of Mainz.
Federal prosecutors declined to confirm those details.
On Thursday, German police conducted raids in Berlin and western Germany against four Algerian men suspected of having ties to IS and plotting an attack in Berlin. One of the men had registered in Germany as a Syrian refugee, police said.
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