Two schools in East Lancashire have already had to send pupils home to self-isolate after positive coronavirus tests.
Children only returned to the classrooms on Monday following a two-month lockdown, but parents have said several pupils from Darwen Vale Academy, and St Peter's Primary School in Blackburn have been told not to come into school.
It is believed that 47 year seven pupils from Darwen Vale High School were told to stay home and self-isolate for 10 days after a student tested positive for the virus.
And a bubble at St Peter's has been advised to self-isolate after a child there tested positive. The school refused to comment.
Aldridge Education, which manages Darwen Vale High School in Darwen, failed to respond to a request for comment before going to press.
One user on social media said: "I feel so sorry for all those children, this affecting them badly."
In an Executive Board meeting on Thursday evening, Cllr Julie Gunn, Blackburn with Darwen Council's education boss said that in general the return to school had been going well across the borough.
She said: "This week we've seen most children returning to schools for the first time really since Christmas.
"That's been going well. We've had some really positive feedback from schools.
"The lateral flow testing is a challenge to roll out and I'd just like to say what a great job schools are doing with that and the pupils themselves undertaking that and committing to do that because we know that they share our view that that's one of the best ways to help keep the cases low, to identify them quickly and self-isolate where required."
Nationally, reports have begun to emerge of children being obliged to self-isolate after receiving a positive Covid test result, even when a second, lab processed test confirms a negative result.
Pupils in secondary schools must undergo lateral flow tests twice a week, which are one of the fastest ways to identify a coronavirus infection, giving results within around 30 minutes of taking the test.
However, concerns have been raised over the accuracy of these tests, with the Royal Statistical Society believing low infection rates among pupils may be producing more false positive results than accurate positive results.
Estimates have put the rate of false positives with rapid tests at a relatively low rate of 0.1 per cent, but given the vast number of students being offered the test, it's believed that thousands of pupils may be receiving false positives and thus having to self-isolate unnecessarily.
These pupils will be obliged to continue isolating even if a later, lab-processed PCR test reveals that they are negative.
The Government has not explained their policy of disallowing a PCR test from overruling the result of a rapid test.
Cllr Gunn added: "I think this demonstrates that the tests are working and that schools are being pro-active in using them.
"We want to flush out the cases so identifying them early reduces transmission.
"Of course, we don't want more disruption for our children but similarly we want to get them isolated so they don't pass anything on, and all we can do is follow the government's advice.
"The schools are working hard to make sure that any children self-isolating are all able to access their learning, and for any parent who has to self-isolate as a result of this and who may find themselves in financial difficulty, they should contact the council as there is support in place for them."
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