The 15 vehicles have been removed from service a year after they were introduced in the city.
First Bus did not provide further details of the problem with the £500,000 buses and said it was being investigated.
A spokesperson said: “We can confirm an issue has been identified with the 15 hydrogen buses and the vehicles have been taken off service until this technical issue can be better understood.
“To minimise the impact of this temporary vehicle withdrawal, we have reallocated low-emission Euro VI buses from our Glasgow fleet and consequently we don’t anticipate any problems for customers planning a journey on our services.”
The buses, whose only emissions are water, started operating between Peterculter and Tillydrone in January last year.
Their introduction followed the first hydrogen-powered single decker buses being trialled in the city in 2015.