Police said the man, who they named as Dragan Mihelic, was arrested on Monday afternoon while trying to cross into Croatia. German authorities suspect he is involved in a betting ring that conspired to fix matches in Europe.
Mihelic is now being held in custody in Zagreb pending an extradition request from Germany.
German authorities have targeted some 200 people in relation to the match-fixing scandal in Europe. Matches in Slovenia are also among those being investigated.
Mihelic is being sought on fraud and money-laundering charges.
Public broadcaster RTV Slovenija said on Tuesday that Mihelic had earlier been interviewed by Slovenian police only to be released.
This was confirmed to RTV by Slovenian police, who said they acted on a European arrest warrant in holding the man in custody. Police told the station that he was later released by an investigating magistrate in Ptuj but did not clarify why.
Slovenian police said on Monday that they had not yet received official notice about the German investigation.
According to reports, up to seven Slovenian premiership matches are being scrutinised by investigators as part of a Europe-wide probe into match fixing.
