Bajevic, 61, fell to the ground after being punched by fans who surrounded the Serbian coach as he attempted to leave the pitch following the 2-1 defeat by second tier side Kallithea.
"What happened is a disgrace for AEK," Adamidis told NovaSport FM radio. "The administration is determined and we will keep the coach. What happened is unacceptable."
Bajevic, who is in a third spell with the club, has endured a rocky relationship with sections of the fans due to previous spells in charge of rivals Olympiakos.
There are fears that this latest episode may lead to his resignation, but Adamidis said the coach would stay on.
"I have spoken to him and he is very shocked," Adamidis said. "But rest assured we will not let him go. We call on the real AEK fans to rid the club of these problems."
AEK have been starved of success in recent years but before Saturday's match they had begun the pre-season impressively, defeating Blackburn Rovers and Rangers in a tournament in Australia.
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