Jeremy Hunt has said giving Shamima Begum access to legal aid to challenge the decision to deprive her of UK citizenship would make him "very uncomfortable".
The foreign secretary said Ms Begum, who left the UK at the age of 15 to marry an Islamic State fighter, "knew the choices she was making", but acknowledged that the UK is a country which believes people should have access to legal representation.
The Daily Mail reports that Ms Begum is now hoping to get legal aid to challenge a decision to strip her of UK citizenship.
Speaking on BBC Radio 4's Today programme, Mr Hunt said: "On a personal level, it makes me very uncomfortable because she made a series of choices and she knew the choices she was making, so I think we made decisions about her future based on those choices.
"However, we are a country that believes that people with limited means should have access to the resources of the state if they want to challenge the decisions the state has made about them and, for obvious reasons, those decisions are made independent from politicians."
Mr Hunt added: "The decision to deprive her of her citizenship was taken by a politician. Obviously the decision about whether she accesses legal aid or not has to be done independently."
Dal Babu, a former chief superintendent in the Metropolitan Police, is a friend of the family.
Mr Babu said that, in order for a proper review to take place, Ms Begum needed to get legal aid.
"I think legal aid is a principle of the British legal justice system. There will be people who can afford to have swanky lawyers, there will be people who have no money who are in desperate situations."
A Legal Aid Agency spokesman said: "We are unable to comment on individual cases.
"Anybody applying for legal aid in a Special Immigration Appeal Commission case is subject to strict eligibility tests."