Rummenigge, who is also Bayern Munich's chief executive officer, last week rejected European Commission (EC) proposals to reform the transfer system, saying that all political attempts to interfere in football had been "catastrophic".
Rummenigge, speaking to two German newspapers last week, also described the Bosman ruling as an "own goal" and said that football had "the perfect system" before the 1995 ruling on the case brought by Belgian player Jean-Marc Bosman.
FIFPro secretary general Theo van Seggelen, who wants a complete overhaul of the transfer system, responded to Rummenigge on Twitter.
"This is really unbelievable," he said, referring to Rummenigge's comment that "football does not need any corrections".
Quoting Rummenigge's remarks on Bosman, he added: "How naive".
In a report last month, the European Commission said that the transfer system needed to be reformed to allow a fairer distribution of wealth in the game.
The report said the current system benefited only the wealthiest players and their agents and the biggest clubs.
Van Seggelen told Reuters last year that the transfer system was to blame for much of football's financial difficulties.
"As long as the clubs believe they can make money from transfers, we have problems," he said.
"Football must grow up as a professional business, it is not a professional business yet, although some people think it is."
The EC has suggested that a "fair play levy" be placed on transfers to encourage better redistribution of funds.