Northlink and Cal Mac will both be included in the investigation
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Former transport minister, Tavish Scott has said Scotland could be due a £20m refund from Europe.
He made the claim after it emerged that subsidies to Northlink and Caledonian MacBrayne ferry services are to be investigated by the EC.
The probe will look into whether state support led to the undue distortion of fair competition.
Mr Scott claims the cost of tendering for new routes was about £20m due to the EU rules surrounding the process.
He claims that the previous Holyrood administration, of which he was a member, launched an expensive tendering process, having been advised that this would comply with EU rules.
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If it turns out that they didn't like that process and they subsequently decide we shouldn't have done that, then I'll be looking for a cheque payable to Scottish taxpayers.
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He told BBC Scotland if that advice was wrong Brussels should refund the £20m cost of the tendering process to the tax payer.
"In those circumstances I think the European Commission should pay the Scottish taxpayer £20m," he said.
"We went through the steps we did as a result of the European Commission.
"Parliament didn't like it but we were told under legal advice that this was the route that had to be followed.
"If it turns out that they didn't like that process and they subsequently decide we shouldn't have done that, then I'll be looking for a cheque payable to Scottish taxpayers."
The Scottish Government said it would co-operate with the European investigation, but pointed out it covered previous Holyrood administrations.
Both ferry companies are part of the Scottish Government-owned David MacBrayne Group.
European Commission Vice President Jacques Barrot stressed the probe would not threaten the future of the services, adding: "I am well aware of the importance of lifeline ferry services to ensure the survival and prosperity of isolated island communities in Scotland.
"This is actually a very important reason why we should ensure full compatibility with EC law and provide legal certainty for the way these services are organised."
A Scottish Government spokesman said ministers were committed to first-class ferry services for remote and island communities.
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