Mrs Morgan had written to Mr Thompson last month demanding answers over the meltdown
Around 2,600 families have been unable to claim two vital childcare benefits because of technical issues at HMRC.
The Mail revealed last week how the Government’s flagship new childcare scheme has fallen into chaos, leaving families out of pocket and children at risk of losing nursery places.
Now the taxman has revealed the full extent of the fiasco, with thousands of parents still waiting for applications to be approved.
In a letter to Nicky Morgan, chair of the Treasury Select Committee, Jon Thompson, chief executive of HMRC, said the taxman has received 1,507 complaints about its new childcare website.
Over 90 per cent were about technical problems.
Mrs Morgan had written to Mr Thompson last month demanding answers over the meltdown.
In his response Mr Thompson said HMRC has received 244,000 applications for one or both of its two new schemes – 30 free hours of childcare and tax-free childcare accounts.
Around 208,000 parents have so far been successful. Of the remainder most are either undergoing additional checks or not eligible.
Some 2,600 parents need a technical issue to be resolved before their application can be dealt with. These cases account for around 1 per cent of all applications.
There are also 18,292 applications that parents have started but not completed. Of these 10,257 are four or more weeks old.
Since the website launched in April it has been down for a total of 160 hours and eight minutes – almost a full week in total.
Just under 5 per cent of parents have experienced difficulties at least once during their application.
Mr Thompson said: ‘As this is a new digital service we sometimes need to take the system down for updates and maintenance.
‘Of this downtime, approximately 50 per cent was between 10pm and 8am to limit the impact on parents.’
HMRC has so far paid £45,687 in compensation to parents affected by these problems
There have also been 257,407 calls to the helpline. although many of these were for general queries as well as parents experiencing technical difficulties.
The average waiting time is one minute 17 seconds, but families have reported having to wait far longer.
The tax-free accounts launched in April are supposed to give parents a £2 top up for every £8 they save towards nursery fees.
However, computer glitches have meant that families have been unable to open an account or access their money.
HMRC has so far paid £45,687 in compensation to parents affected by these problems.
Meanwhile, 4,227 parents have already closed their accounts since they launched five months ago.
The taxman said around 2,000 parents have done this because they want to claim tax credits instead.
The second scheme, due to launch in September, will double number of free childcare hours for working families with children aged three and four.
HMRC said it is on track to provide 200,000 of the codes needed to claim this perk by August 31
HMRC said it is on track to provide 200,000 of the codes needed to claim this perk by August 31.
But many families are still waiting with just days to go until the deadline and could miss out on nursery places or not get the hours they need as a result.
The taxman urges families experiencing technical problems online to call its helpline on 0300 123 4097 so it can issue the code needed over the phone.
Mr Thompson said: ‘I take the committee’s concerns very seriously, and I am very sorry that some parents have experienced problems and have not received the service we aim to deliver. We are working to improve the way the service works.’
Mrs Morgan said: ‘Whilst it is welcome that HMRC has made “significant improvements” to the website since it was launched in April, thousands of parents are still unable to apply for the childcare to which they are entitled in the way that the Government has envisaged.
‘Clearly further improvements are still required. The committee will no doubt want to question representatives of HMRC on the technical issues with the Childcare Service website when they are called to give evidence.’
A spokesman for the committee said there was no set date for future evidence sessions yet and it will be decided in September or October.
Neil Leitch, chief executive of the Pre-school Learning Alliance, said: ‘We recognise that HMRC are working hard to rectify the problems with the website, but the fact remains that thousands of parents and childcare providers have been adversely affected by these glitches.
‘Both 30 hours “free childcare” and Tax Free Childcare were key Conservative manifesto promises, which the government seem wholly unprepared to deliver.
‘The very least we expected was investment in an IT system that parents are able to use, and through which childcare providers are able to receive the payments that their businesses rely on.’