The midfielder has been frozen out at the Allianz Arena and while his captain has some sympathy for his team-mate's plight, he says that the coach's authority has to be respected
The Germany international reacted angrily to being substituted during the recent 2-1 win over Stuttgart and was left on the bench for the two subsequent Bundesliga games.
While his captain can understand his team-mate's frustration at being frozen out, he says that Pep Guardiola's authority must be respected.
"It's not nice for Toni, that much is clear," Lahm told reporters. "But the coach makes the decisions and everyone has to accept them."
Meanwhile, former Bayern and Germany midfielder Stefan Effenberg has also voiced his sympathy for the 24-year-old Kroos.
"This is a bitter pill to swallow for Toni," he said in his capacity as a pundit for Sky.
"He always played under [former boss Jupp] Heynckes, but that's over. It's not favourable because the World Cup is around the corner."
Kroos recently revealed that contract renewal talks with Bayern have reached an impasse, with his current deal set to expire in the summer of 2015.