The 67-year-old former Real Madrid boss says he was frustrated by the timing of the former Blaugrana coach's appointment at die Roten
It was announced last week that Guardiola would succeed Heynckes as Bayern boss, but the former Real Madrid coach believes there would have been less impact on his team had the announcement come earlier.
"It would have been better to do this in the winter break. Before Christmas, before the holidays," Heynckes told Sky.
"This is due to the media hype that might interfere with the normal working day."
In the wake of Bayern's 2-0 win over Greuther Furth, Heynckes also responded angrily to claims he was not in control of his team.
He added: "I am the boss. Anyone who knows me knows I am the boss here. I have been the boss everywhere - no matter where I have worked."
Meanwhile, Franz Beckenbauer has defended Bayern's timing of the announcement, insisting Guardiola's stature within the game affected when his appointment could be confirmed.
"If somebody is as high calibre as Pep Guardiola, you should not be surprised if it is the big issue. Now, it has to be Jupp. But he doesn't seem happy," the World Cup winner told Bild.