Some 100,000 higher-earning families who have not registered to opt out of receiving child benefit will be in line for fines if they fail to contact the tax authorities by the deadline of midnight tonight.
Following George Osborne's decision to end universal child benefit, households containing a parent earning more than £50,000 will for the first time lose part of the payment, while it is being withdrawn altogether from those with an adult with a taxable income of over £60,000.
Those parents affected by the changes were given the choice of either opting out of receiving child benefit altogether or carrying on receiving it and paying any charge at the end of each tax year under self-assessment.
But around 100,000 parents have neither registered for self-assessment nor opted out of the benefit - worth £20.30 a week for the first child and £13.40 for each younger sibling.
Penalties for missing today's tax return deadline start at £100 for one day's delay, with a further £10 for each of the following 90 days, and an additional £300 - or 5% of the tax due - after six months.
But she made clear that eyebrows would be raised if anyone claimed that they had simply not heard about the change.
"We've been writing to people since autumn of 2012 so those people affected will have had at least three letters from us and we've done advertising campaigns through 2012 and 2013, so I think we've got the information out there," Ms Owen told BBC Radio 4's Today programme. "I think it's important to recognise that 90% of people have registered and understand what their liabilities are, so it's just those last 10% we still need to contact."
Ms Owen urged anyone who has not yet registered to get in touch with HMRC as soon as possible.
She said: "Today is the deadline by which you have to send us your tax return and pay your tax. The difference this year is some people who chose not to opt out of receiving child benefit had to register to pay a charge through their self-assessment tax return and today is the deadline for getting that done.
"Of about one million people affected, about 100,000 still haven't registered with us.
"I would encourage anybody who thinks they are affected to get in touch with us. The first thing to do is to let us know if you think you are affected and we will register you, and then we can arrange for you to complete the tax return online and get that tax paid in time.
"They could be penalised because October was actually the time by which they had to tell us they were affected, so that's a failure to disclose information to us. But I would still say do get in touch with us, because from tomorrow onwards not having paid your tax means you start incurring a £100 penalty fine plus interest after that, so the sooner you contact us the better."