Rene Schnitzler, who played for the club when they were still in the second division, told Stern magazine he accepted the money from a Dutchman working with a betting outfit, although he denied influencing any matches.
St Pauli said Schnitzler, who is now 25 and dropped into regional football after leaving the club in 2009, ended up not playing in three of the five games, which were all away.
"Even when no manipulation has taken place, it is a kick in the face," St Pauli team manager Christian Boenig told reporters.
"We didn't notice anything conspicuous and neither did the other players, had we done so we would have reported it.
"But it's a very uneasy feeling when a player whom we've discussed tactics with and worked with in private is connected with the betting mafia.
"We knew Rene had problems and we had offered him help, but we were not aware they were so deep."
Coach Holger Stanislawski added: "It's simply very disappointing when something like this happens."
German media said the matches were against Hansa Rostock, Duisburg, Augsburg and two against Mainz 05.
Schnitzler said he was addicted to gambling.
"Since I was 18, there has hardly been a day when I did not bet," he said in an excerpt from the interview which Stern's website said would be published in full on Wednesday.
St Pauli said they were cooperating with prosecutors in Bochum, who in 2009 exposed a match-fixing ring with more than 200 members who tried to fix games across Europe.
German media said Schnitzler does not currently have a club.
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