The Education Secretary said “nervous” parents will not be punished if they keep their kids home.
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But he said the Covid-19 crisis could last another year and schools must start gradually reopening to stop kids falling “tragically” behind.
Primaries will be allowed to stay shut past June 1 only if they have “practical problems” sorting out the new class size cap, he said.
Mr Williamson went on: “When you see other countries around the world who are quite a number of weeks ahead of us in terms of bringing schools back, you see small numbers of pupils in school for the first few weeks.
“And then that rapidly starts to increase when people realise how much their children are missing out by not being in school.”
Boris Johnson faced down hard-line teaching unions to announce at Sunday night’s Downing Street press briefing that he is pushing ahead with plans to send children back to class from next week.
Mr Williamson insisted England is taking a “cautious” approach by sending only a few year groups back on June 1.
He added: “The virus crisis could be with us for a year or more.
“If we don’t bring children back, how much further they fall behind will be incredibly tragic.”
And he warned primaries that while they will not be punished if they don’t meet the June 1 deadline to reopen, they need to have a good excuse if they miss it.
He told BBC Breakfast: “We understand there are practical problems in schools and we are working with them closely to work out those practical problems.
“But we don’t want to see schools not opening for reasons that aren’t practical reasons.
“If they work with us we will make sure schools are open. I can’t see a situation where a school cannot open.”
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