The decision follows a review of the Scottish Government’s support of routes to the northern and western Isles.
But the commission has called for a public tender to be carried out for the Gourock-Dunoon ferry, operated by state-owned CalMac.
The Scottish Government welcomed the findings.
“This report allows us to maintain the support which ferries receive at present while also allowing us to look at what further improvements can be made to these lifeline services as part of our ferries review,” a spokesman said.
Scotland’s main private ferry companies, such as Western Ferries and Pentland Ferries, had complained about CalMac’s dominance.
The EC launched the review in April last year.
The ruling states: “The public service obligations for the western and northern islands were legitimately defined and entrusted on the operators.
“The commission also came to the conclusion that the compensation paid to the operators in the past did not exceed the costs of providing the public service entrusted on them.
“Lastly, it did not find sufficient evidence that these operators had engaged in any type of anti-competitive behaviour that might have unduly distorted competition.”
Clyde and Hebridean routes are offered as a package of 24, with the exception of Gourock-Dunoon.
The Government said this is the best way to prevent private operators “cherry-picking” the most profitable routes, safeguarding the future of lifeline services which need subsidised to survive.
The Gourock-Dunoon route will now be put out to public tender - today’s findings said that the absence of such a tender is unlikely to be compatible with state aid rules.
SNP MEP Alyn Smith, who has campaigned to secure the island ferry services, said: “After decades of jumping through EU legal hoops this is a positive decision for Scotland’s remote and island communities.
“Our ferry services are essential and I welcome the commission’s confirmation that the Scottish Government’s actions are right and appropriate to secure the future of our ferries.
“The pro-active approach of the Scottish Government to securing our ferries future has paid off.”
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