Amber Rudd told MPs of her “bitter regret” that she failed to take the situation seriously when she first heard about it.
But she insisted there is no evidence that any Caribbean-born Brits have been kicked out of the UK as a result of the scandal.
Ms Rudd – who faces calls to quit as Home Secretary – was hauled in front of the Commons’ powerful home affairs committee this evening.
Asked by chair Yvette Cooper when she first found out about the problems faced by the Windrush generation, the minister replied: “I became aware over the past few months that there was a problem of individuals as far as I was seeing.
“I bitterly, deeply regret that I didn’t see it as more than individual cases that had gone wrong that needed addressing, I didn’t see it as a systemic issue until very recently.”
Asked whether any of the middle-aged Brits affected had been deported, Ms Rudd said: “The answer to that is, not as far as we know.”
She said officials had examined 7,000 deportation records dating back 18 years, and not found anyone from the Windrush generation wrongly kicked out of the country.
But she admitted the Home Office still has no idea how many Caribbean-born Brits have been wrongly detained by immigration authorities – like grandmother Paulette Wilson, who spent a week in detention after being told she was in the UK illegally.
Ms Rudd said she was “shocked” by Ms Wilson’s case, adding: “I’ve put in measures so that there are more checks in place so that an individual such as she was is not locked up.”
And she confessed the Home Office should have been much quicker to notice there was a problem – saying: "To be honest, I think there were warning signs on this from the noughties. There were signs that were arising ten, 20 years ago."
At the hearing Glynn Williams, the senior civil servant in charge of border control, revealed that nearly 1,400 Windrush migrants have already contacted the Home Office’s special helpline set up last week.
Of those, 23 have so far been handed the documents they need to stay in Britain.
Ms Rudd insisted the Windrush crisis had not convinced her and Theresa May to drop the migration target, which aims to cap net migration at 100,000 a year.
She told the committee: "It's wrong to think the net migration target is the problem here. The problem here is that people were not properly documented."
Asked if she has talked to Mrs May about scrapping the target, Ms Rudd replied: "I have not discussed that with the Prime Minister."
The Windrush scandal blew up into a political crisis last week after a group of Commonwealth leaders demanded to meet the PM to discuss how to get justice for those affected.
Mrs May initially refused their request – but was then forced to back down and apologise as members of the Windrush generation continued to come forward.
Some Caribbean-born Brits were denied benefits or medical treatment, while others lost their jobs after being unable to produce the right papers to prove they are here legally.
Today it emerged the problem stretches as far back as 2011 – after a letter written by the PM's former deputy Damian Green came to light.
Mr Green, then the immigration minister, wrote to Labour MP David Lammy after he requested help on behalf of his constituent William O'Grady, who moved from Jamaica to the UK in 1959.
Mr O'Grady had been unable to work or claim benefits for seven years because he lacked the proper documents – and Mr Green suggested it was his fault for not getting the paperwork decades earlier.
The minister wrote: "Having settled status would mean that he would be able to live and work in the UK without restriction."
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