Government wanted to rush the legislation through before the close of Parliament, but the Conservatives blocked the proposals.
Fiona Nicholson, trustee of home education charity Education Otherwise, said the amendments had prevented "a grave injustice being foisted on tens of thousands of home-educating families". She described government's attempt to introduce the new measures as a "sorry episode".
"Ministers have belittled the enduring commitment to children's rights shown by home educators," she said.
But Children's Secretary Ed Balls accused the Conservatives of being "profoundly misguided" in a letter to his shadow counterpart Michael Gove.
He warned children would be at risk without the home education registration scheme. "We have always been clear that the vast majority of home educators do a good job and that they have nothing to fear from the proposals we brought forward," he explained.
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