The former Germany international thinks the midfielder has made life complicated for himself with his reaction to being taken off against Stuttgart.
The 24-year-old midfielder lost his starting berth after publicly showcasing his frustration with his substitution in the 2-1 win over Stuttgart last month, while the breakdown of talks over a new contract has also reportedly caused consternation at the Allianz Arena.
Consequently, Helmer thinks that the Germany international might have to settle for a spot on the bench for the foreseeable future.
"Pep gave a signal to the entire team by dropping Kroos. The fact that Toni didn't start in the past few games is almost certainly related to his reaction after he was taken off against Stuttgart," the 48-year-old told AZ. "Kroos is the type of player that Guardiola likes. He was an undisputed starter in the first half of the season. But that was also the result of Thiago Alcantara and Mario Gotze's injury problems.
"He could be in trouble from here on. Pep also has Philipp Lahm, Thiago and Gotze who can feature in midfield. And those players are not the worst around ..."
Kroos has a contract with Bayern until June 2015 and both parties have so far been unable to reach an agreement over a new deal because of the player's wage demands.
Clubs such as Manchester United and Juventus are reportedly closely monitoring the Germany international's situation at the Allianz Arena.