Farina, who was playing for second-tier Gubbio when he refused a 200,000-euro ($261,300) offer to fix an Italian Cup match, has been made a FIFA ambassador but has been unable to find a new club after being released at the end of last season.
"This is something absolutely incredible, it is something that could only happen in a game and...it should not," said Blatter, struggling to choose his words after being asked to comment on the situation by an Italian journalist.
Blatter initially mentioned Farina's case without referring to him by name.
"We have to protect the players who disclose match-fixing," he said. "We have had some feedback where players disclosing some activities...have not been accepted again as players.
"We have to protect the players and the players also have to be protected in their clubs, their leagues, their federation. We at FIFA cannot make an umbrella over all the players, it is not possible."
Blatter admitted that players were often vulnerable, especially if they were at financially troubled clubs and were not being paid on time.
They are not happy where they are...there are some players still waiting for their wages and so on, therefore it is not an easy issue but we have to protect the players, it is essential and this is what we have to do," he said.
Farina told police he had refused the offer to fix an Italian Cup match between Cesena and Gubbio on Nov. 30 last year. He was later invited by Italy coach Cesare Prandelli to join his squad.