First Minister Mark Drakeford says some schools need to start planning for pupils to return to online learning.
Staff illness and shortages due to teachers self-isolating mean there could be home learning in some areas, but he said that decisions would be made by individual councils rather than the Welsh Government.
Earlier this month, the Welsh Government did tell headteachers to delay the start of next term for pupils and use the first two days back for planning, including possible remote teaching. And Wales' education minister Jeremy Miles warned all schools may be unable to open fully.
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In an interview with WalesOnline, Mr Drakeford was asked about the return of schools and he said: "The first two days of term are planning days.
What the education minister Jeremy Miles has asked schools to do is to plan for two possible futures: the one in which children can still be in the classroom, where there are sufficient staff to be there to be able to provide face-to-face learning, but to maximise the protection that can be put in place inside the classroom to keep students and staff as safe as possible.
"But we recognise that there will be some schools where, because Omicron is so transmissible, there will be staff who will be ill so it won't be possible for every child to be in the classroom and therefore that a return for some students for a shorter period of time as possible to online learning may have to be there as well.
"So schools will be preparing for both of those eventualities.
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"The decision in the end is best made at that school level because the circumstances will be different from one school to the next. And head teachers will make that decision together with their staff."
You can read the full interview with the First Minister here.
Mr Drakeford also told BBC Wales the decision on whether schools could fully reopen was best made by "people who are as close to it as possible" as "different schools face different challenges".
He added: "We've asked schools to prepare for how they can reopen and have children back in the classroom - what level of protections do they need to build in for that? But in some places, because teachers are ill and other school staff aren't able to be there, they will have to plan for some period where some children will have to be taught remotely again."
Before Christmas many schools have been struggling with staff and pupils off and a shortage of supply cover, and schools in some areas closed early. You can read more about that here.
Laura Doel, director of head teachers' union NAHT Cymru, said: "The availability of staff is the biggest threat to education in January. Without the workforce fit and well, learners cannot go back to the classroom. If regular LFTs are to be part of the package of mitigations it is vital that schools have a supply ready for reopening."
She added remote learning should be a "last resort".
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