E-Clear, which handled online sales for Flyglobespan, withheld 35m from the Edinburgh-based travel firm before its collapse last month.
Administrators PricewaterhouseCoopers said it was clear the money was "no longer there".
It means that 15,000 customers who paid for flights with a non-Visa debit card are almost certain to lose their money.
E-Clear owner Elias Elia has blamed a "Northern Rock-style" run on his firm for its downfall.
The Scottish Government said it was pressing the UK Government for a full investigation.