Kids Active Southern River was found by the State Administrative Tribunal to have breached education and care services laws in relation to the incident in September last year.

The Department of Communities said a group of children had returned to the childcare centre at about 1.30pm after an excursion to the Perth Museum.

Staff members did not check the bus after the children got off. A head count was conducted, but it was not recognised at that point that a child was unaccounted for.

Another head count and roll call was conducted at about 3.35pm, and it was then that staff noticed the boy was missing.

After a search of the premises, he was found on the bus at about 3.45pm.

The temperature on the day was about 18C, with the boy described as upset, hot and sweaty.

As well as the fine, the service was suspended and required to implement a number of changes to its practices before the suspension was lifted.

"To receive a report of a child being left in a locked bus for over two hours is quite confronting, even for our experienced investigators, as we have seen in other states it can have tragic consequences," Department of Communities' acting deputy director Damien Stewart said.

"In this case, numerous mistakes were made, from the moment the bus returned to the service from the excursion.

"Firstly, staff members failed to check the bus and, subsequently, opportunities to identify that a child was missing weren't taken."

Mr Stewart said the case was the 11th time in the past six years where action had been taken over children being left on buses.

Australian Associated Press