Javid said that so far, Home Office officials had identified 63 records of people who were deported to the Caribbean and who may in fact have been entitled to remain in Britain under rules applying to Windrush immigrants.
Mr Javid revealed the figure in his first appearance before the Commons home affairs committee since replacing Amber Rudd who resigned last month over the Windrush scandal.
He said the figures were provisional.
Thirty-two were deported foreign offenders and a further 31 people were administratively removed after being told to leave by officials, rather than following a court order.
He did not know how many people had been detained because of false suspicions over their immigration status. Many came to the United Kingdom legally as children but have no formal documentation, which has also led to them being refused jobs or healthcare.
Javid said the Home Office had identified cases where people were removed who may have come to the United Kingdom legally from the Caribbean.
In three cases, the person does have a legal basis to stay in Britain, while nine cases are ongoing.
"We have found 63 cases where individuals could have entered the United Kingdom before 1973" and were eligible for protection from removal, Mr Javid told MPs.
Prime Minister Theresa May has announced a government review to understand how members of the Windrush generation "came to be entangled in measures" created to tackle illegal immigration.
Labour MP David Lammy, who has campaigned vigorously on behalf of those affected by the scandal, said the admission was "truly a day of national shame" and called for an explanation from Theresa May.
According to a letter sent to MPs on the committee by Home Office permanent Secretary Sir Philip Rutnam, there have been 17 cases where deported Windrush immigrants have returned to the United Kingdom since 2015.
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