The 69-year-old thinks the Champions League holders could decide to sell the midfielder in order to set an example.
Negotiations between Kroos and Bayern over a contract renewal have so far been unfruitful as the Bundesliga champions are reluctant to meet the 24-year-old's wage demands.
Netzer has warned the midfielder that he is not indispensable at his current club.
"Kroos is playing a risky game at Bayern. The club is determined not to pay huge wages to all their players in order to stay financially healthy," Netzer writes in his column for Bild. "We could see this become a situation where Kroos forces Bayern to set an example. He might be overrating himself a bit in a way that his wage demands do not reflect his worth to the team.
"He'd act wisely to have a good look at the squad and re-think his own situation.
"I would advise Toni Kroos not to overplay his hand. He could enjoy a lot of success at Bayern. It's not easy to leave a big club like Bayern. There are a few players that cannot be replaced, but Kroos is not one of them."
Kroos' current deal with Bayern is due to expire in the summer of 2015 and Manchester United is reportedly monitoring the midfielder's situation at the Allianz Arena.