The flight took off at 6.30am this morning despite a Court of Appeal judge ordering the Home Office not to deport many of the detainees amid concerns over their access to legal advice
It is not known how many people were on board or where the plane took off from.
The court order on Monday stopped the government deporting some of those due to leave, amid concerns they may not have had access to legal advice.
Chancellor Sajid Javid said no British nationals or anyone protected by the court ruling were on the flight.
All of those being deported are Jamaican nationals who have been convicted of criminal offences and served prison sentences of 12 months or more.
“It is absolutely right that when they have served their sentence that we send them out of the country,” Mr Javid told BBC Radio 5 Live.
“They are not British nationals, they are not members of the Windrush generation, they are all foreign national offenders.”
The flight had been due to leave for Kingston at 6:30 GMT on Tuesday.
On Tuesday, the Home Office said: “We make no apology for trying to protect the public from serious, violent and persistent foreign national offenders.
“The court ruling does not apply to all of the foreign national offenders due to be deported and we have therefore proceeded with the flight.”
“The court ruling does not apply to all of the foreign national offenders due to be deported and we are therefore proceeding with the flight,” it said.
Bella Sankey, director of Detention Action, said the Home Office decision “defies belief”. The charity said it was not clear if any of those covered by the court order had been removed. Some of those ruled not to have had access to proper legal advice were taken to the airport in the early hours of the morning but then returned to the centre, it said.
The Home Office did not offer further details. It has said that it is bound to deport the ex-offenders under the UK Borders Act 2007, which requires anyone receiving a prison sentence of more than one year to be automatically liable for deportation, with little possibility of appeal.
More than 150 MPs signed a letter calling for the charter flight to be suspended pending the publication and implementation of the Windrush Lessons Learned Review, which was commissioned by the government following the 2018 scandal, in which Caribbean nationals who were denied access to services, were detained or deported despite long-term residency in the UK.
An extract of the draft report released last week recommended the government stop deporting people who have been in the UK since childhood, prompting critics to argue that the charter flight was in violation of the review findings.
Although the Home Office insisted that all those on board were “serious criminals”, many have committed only minor offences.
There had been calls for the government to suspend the flight until a report on the Windrush scandal has been published.
A leaked draft of the report said the government should consider ending the deportation of foreign-born offenders who came to the UK as children.
The advisory panel of a review into the Windrush scandal, including a former senior immigration judge, has warned against the resumption of mass deportation flights to Jamaica until after its report is published.
MPs, support services for migrants and activists have criticised the flight, pointing out that it is taking place before the publication of the long-delayed “Windrush lessons learned” review.
Campaigners argued that most of the detainees due to be deported had spent the majority of their lives in Britain.
Labour’s shadow home secretary Diane Abbott said removing the detainees was “unfair”, adding: “Many of the proposed deportees came here as children and have no memory of Jamaica.”
But Home Secretary Priti Patel said many of those on board were guilty of “serious offences”, including rape and dealing class A drugs.
Every person on the flight had “received a custodial sentence of 12 months or more”, she said.
Therefore under legislation introduced by the Labour government in 2007, Ms Patel said, “a deportation order must be made”.
‘I have no-one in Jamaica’
One of those who had been due to be deported on Tuesday is father-of-five Howard Ormsby.
He was jailed for 18 months after he was convicted of possession with intent to supply class A drugs and he was released in December.
“I came here at the age of 15 with my older sister and I’ve been here 18 years of my life,” the 32-year-old said, speaking to the BBC’s Victoria Derbyshire show from a detention centre at Harmondsworth, west London.
“I’ve never tried to deny the fact I’ve made a mistake, but everyone has a chance to right their wrongs.
“I have all my family here – I have no-one in Jamaica.”