Shamima Begum, who had left London as a 15-year-old in 2015 to join the Islamic State group, had pleaded with British authorities before her baby was born to let her return to the U.K.to raise the child.
It comes as a top Muslim leader called on Muslim countries to "adopt" Islamic State bride Shamima Begum following the cancellation of her British citizenship.
Begum, a 19-year-old British teenager of Bangladeshi descent, gave birth to her son in a Syrian refugee camp in February.
Mr Hunt continued that when Begum first travelled to Syria in 2015 she knew she was going to join a "terrorist organisation" and that "she was going to a country where there was no embassy, there was no consular assistance, and I'm afraid those decisions - terrible though it is - they do have consequences".
Camera IconCCTV of Shamima Begum leaving at Gatwick Airport
Quoting legal sources, the paper named the women as Reema Iqbal, 30, and her sister Zara, 28, whose parents are originally from Pakistan.
In an interview with a reporter from the Times of London, who found her in the Syrian camp, she said she wanted to return home in large part because of her son's health. Decisions to withdraw citizenship from individuals were evidence-based and not taken lightly, it added.
"It was hell on Earth and every single one of them made it so", he said, asking sarcastically if perhaps local victims of the jihadi women should "apologize for disturbing their stay there".
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The disclosure came as a row intensified over the death of a three-week-old baby whose mother Shamima Begum had been stripped of her British citizenship.
The challenge faces other European countries as the final IS stronghold in Syria is on the brink of falling, giving its fighters and their often youthful spouses no place left to hide.
Prior to the child's death, Ms Begum's sister, Renu, wrote to Mr Javid on behalf of the family challenging the decision to revoke her citizenship.
Jarrah died of pneumonia on Thursday, according to a medical certificate.
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Shadow home secretary Diane Abbott also criticised the actions of the Home Office.
The 19-year-old had controversially said she wanted to return to the United Kingdom after feeling to Syria at the age of 15.
"No dignified self-governing state should abandon responsibility for its own citizens in this way, trying to dump them on to poorer countries with failed security arrangements", he told The Observer.
The infant's father, a Dutch ISIS fighter who was captured and is being held in a nearby prison, was informed of the baby's death. The Begum family's lawyer, Tasnime Akunjee, said: "They are utterly crushed and despondent at the moment".
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"The security services came to speak to me and I was honest, I told them my whole story so now it's up to them to judge". Begum has previously lost two children.