Pupils will not have to socially distance on some home-to-school buses but may have to wear masks.
Some local authorities are issuing guidance for bus users as they plan the return to classes next week.
Pembrokeshire council published advice for parents on Monday, saying secondary pupils would have to wear masks and recommending primary pupils also do so.
But not all councils are making wearing masks mandatory and some have yet to publish their latest guidelines.
Bridgend council said it would provide “sufficient” buses to cover all the pupils who needed it but did not clarify if pupils would need to socially distance on board.
However, it is not mandating the use of masks.
Face coverings on public transport for anyone over the age of 11 became law in Wales in July but services such as dedicated coaches for home-to-school transport have been made exempt.
It is up to individual local authorities to decide whether to require secondary pupils to wear masks on its contracted school bus services.
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Cardiff Council said it would provide masks to all secondary school pupils on school transport.
Ceredigion council said it was also expecting pupils to wear face coverings on buses and in taxis for home-to-school transport as social distancing was not required for school buses.
And Vale of Glamorgan council is making it mandatory for children aged 11-plus to wear facemasks while travelling on its contracted transport services.
The Welsh Government published advice for schools in July which included some guidance on home-to-school transport.
Pupils catching commercial bus services to get to school already need to wear masks.
Parent Tracey Elsam, from the Vale of Glamorgan, said: “I do understand that people will be nervous about their children going back but I do think it is as safe as it possibly can be and they really, really need their education.”
A spokeswoman for Bridgend council said it was in contact with transport providers about trying to co-ordinate with schools “to ensure that learners in the same learning groups sit together where possible on dedicated school transport”.
Advice by Pembrokeshire council still encourages parents to take their own children to school by walking or cycling, or driving if necessary, but parking away from the school and walking the last section.
The advice for buses said: “There will be no social distancing between pupils on school transport, however, social distancing will be maintained between the driver and pupils on large school buses.
“This will mean that no pupils will be allowed to sit on the front row of seats.”
Secondary pupils who do not use a face covering could have their transport place withdrawn, it added.
It advises pupils to “try to maintain” social distancing at bus stops and use hand sanitiser when getting on board and go to the furthest seat back possible to “avoid the need to pass other pupils”.
Guy Woodham, cabinet member for lifelong learning, said: “While social distancing may not be possible for pupils and students aboard education transport, the measures introduced following discussions between council officers and school transport providers will help keep everyone as safe as possible.”
Cardiff Council also said it was “treating each mainstream school bus as its own bubble as it will be the same children travelling each day”.
What do the bus operators say?
Shon Rees, managing director of Midway Motors Coaches in Crymych, Pembrokeshire, which runs up to 20 school buses, said the council decision to make face masks mandatory was “fantastic” and would make drivers feel safer.
He told BBC Radio Wales’ Gareth Lewis programme that buses would carry a supply of masks so pupils without one would not be left at the roadside.
Chris Owens, managing director of Llandudno-based Alpine Travel, said his services to more than 40 schools in the area would be running as normal when pupils return in September.
He said they had had lengthy discussions with the Welsh Government and coach operator associations about how to manage the coronavirus risk.
“You have the risk of transmission between pupils, but we have a duty of care towards our employees,” he said.
As in Pembrokeshire, none of the front seats of the coaches will be occupied by pupils to allow for distancing from the drivers, who will run their window demisters constantly to provide a flow of fresh air into the coach, Mr Owen explained.
He said while it was not compulsory, he hoped local authorities in his area would require the use of face masks by students.
“It comes down to being in the gift of local authorities [making] students wear face masks on coaches,” he said.
“We have done a lot of work and we’re very confident that transport will be as safe as it can be.”
A Welsh Government spokesperson said: “We are working closely with local authorities, the Confederation of Passenger Transport and bus operators to ensure safe and accessible school transport.”