Buses have been driving past stops leaving children unable to get to school or arriving late, a parent said.
Covid-19 social distancing measures have meant buses have 50% reduced capacity, affecting out-of-catchment pupils who rely on timetabled services.
A parent in Long Stratton, Norfolk said it was disrupting her son's ability to get to sixth form in Norwich.
First Eastern Counties said it was "sorry we're in this position" and it had put on 28 extra buses for pupils.
Parent Helen Menary, said before lockdown in March the commercial service, which was not a dedicated school bus, ran smoothly, but now full buses were not stopping and she has had to take her son to Norwich often.
"I know it's difficult for the bus company, but I think something could have been done in preparation," she said.
"Since he returned in September most days the bus has gone straight past or has only taken a few passengers and he has been left at the stop.
"Often they've told us a relief bus is following, but most of the time it doesn't come."
David Jordan, a spokesman for First Eastern Counties, said: "We are sorry we're in this position, but this is largely due to the necessity for social distancing and only carrying 50% of normal capacity."
The company said it had put on 28 extra buses across its network solely for out-of-catchment school pupils who relied on commercial timetabled services, which meant they did not have to compete for seats with other passengers.
"Also, the bus between Long Stratton and Norwich starts in Harleston and is usually a single decker because of low trees along its rural route," Mr Jordan said.