Families were given until the end of today to opt out of receiving the state help or register for income tax self-assessment so some or all of it can be clawed back - or face possible fines.
Officials say that punishments are unlikely to be imposed on anyone who complies by the end of January, but HMRC chief executive Lin Homer said many thousands had still not done so.
"We think there are about 200,000 people who need to get off their backsides and do something," she told BBC Radio 5 Live.
"HMRC is committed to helping people pay the right amount of tax and urges parents who have been affected by the changes to child benefit to register for self-assessment," said Ms Homer.
"We know that lots of people leave it until the last minute."
Her comments came as the TUC attacked the "complicated and confusing" letters sent to households which it said could lead to some people still entitled to the benefit opting out with "disastrous" consequences.
Those on £50,000-plus have been stripped of 1% of the help for every £100 earned over that level to prevent a dramatic "cliff edge" loss.
The TUC said letters were being sent " arbitrarily to people unaffected by the change" and failed to make clear to parents what they needed to do.
It raised particular concerns over instructions related to ensuring stay-at-home parents did not lose out on credits required for them to qualify for a state pension.
General secretary Frances O'Grady called on the Government to restore universal child benefit and condemned the implementation of the policy as "a mess".
"Quite apart from the fact that the decision to withdraw the benefit is unfairly hitting single parents, many families where one parent earns more than £50,000 are - even at this late stage - still unaware that unless they've visited the HMRC website by the end of today they may be fined,"she said.
"To make matters worse, HMRC isn't only sending letters to those parents affected by the change.
"We've been hearing about parents earning below the £50,000 threshold who have been written to, as have mums and dads whose children are too old to qualify. Even childless couples have been receiving letters.
"There's also a risk that some vulnerable parents earning way below £50,000, and who get the HMRC letter by mistake, could think they are about to lose their child benefit, and rather than pay a fine, opt out of child benefit - with potentially disastrous consequences.
"Although registering for self-assessment only takes a matter of minutes, trying to work out whether to keep on receiving child benefit or stop the payments altogether is not easy. The complex changes and the confusing way in which affected parents have been informed makes it likely that many families where the mum or dad earns more than £50,000 may miss today's registration deadline."
© 2013 Press Association