This comes after Boris Johnson ordered areas in Greater Manchester back into partial lockdown in a bid to stop a second wave of coronavirus.
In areas such as Bury, Trafford, Salford, Bolton and Rochdale people must only interact within their support bubble but schools remain open.
Co-op Academy in Swinton was worst affected after positive cases in Year 7 and Year 10 meant both year groups were sent home on Monday morning.
While the school initially said siblings should also stay off, parents have now been told that brothers and sisters can attend.
Speaking to Manchester Evening news a parent from Co-op Academy Swinton said: “What’s the rules if we just want to keep our children off for the foreseeable?
“This is just going to continue and they’re going to just keep getting sent home.
“Day three and it’s happened. It’s going to be a weekly occurrence. I am not putting my child at risk, she has severe asthma. So I don’t want her going back.”
Professor Kate Ardern, Wigan Council’s director for public health, says that a rise in cases is ‘inevitable’ as children return to class.
She said: “The return to schools will inevitably see a rise in cases across the country, but it is important to note that all the relevant and necessary safety measures are in place and being followed strictly.
“We are supporting the school with advice and guidance at this time.
“The school remains open and it is not necessary for any other child to self-isolate, stay away from school or to be tested, unless they develop symptoms of Covid-19.”
A spokesperson for Trafford Council said: “Our Public Health Team is working closely with three Trafford primary schools where a small number of pupils have tested positive for Covid 19.”
They added: “The schools have informed all parents and the children and staff in the affected classes have been asked to self-isolate for two weeks in line with government guidance.
“The schools in question will remain open to other pupils during this time and the affected areas will be deep cleaned.
“The health and safety of pupils and staff at all our schools remains our number one priority and our Public Health Team will continue to work closely with school leaders to provide them with the necessary support.”