Elizabeth Jarvie, Sheriff at Edinburgh Sheriff Court, said it was "imperative" children had the right to "due process without any hindrance".
The Executive tried to insist that teenager Jacqueline Shields should pay a 5,000 court bond before she could press ahead with her action.
She claims the Executive is failing to protect her from homelessness because her father is struggling with debts and is locked in a dispute with the Scottish Legal Aid Board.
But an Executive spokesman denied the tactic was aimed to halt the case.
Defending costs the taxpayer "tens of thousands of pounds", he said.
"We have to protect the public purse and believe it right to ask for some money to be paid into court to cover expenses."
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