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 he acknowledged that having access to representation was a key part of the British legal system.
Ms Begum is hoping to get legal aid to challenge a decision to strip her of UK citizenship according to reports.
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."
Speaking on BBC Radio 4's Today programme, 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.
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He told Today that Ms Begum should have legal aid to make sure the correct process is followed.
Mr Babu said: "Isis is a murderous organisation. They are a horrendous organisation and I don't think anyone in their right mind would be joining that organisation.
"She was a young woman. She was 15 when she was groomed. The police were aware of this, the counter-terrorism police were aware of this, the school she was at was aware of this, and the social workers at Tower Hamlets Council were aware of this.
"There has been no serious case review. Normally, when a young person dies as a result of failures in safeguarding, there is a serious case review."
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.
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"Anybody applying for legal aid in a Special Immigration Appeal Commission case is subject to strict eligibility tests."
