Eurotunnel has been given two months to respond to a European Commission request to lower charges for passengers and freight trains using the Channel Tunnel.
The high track access charges result in more expensive Eurostar tickets and the Commission said the company faces potential court action.
"Access charges for passenger services and freight are much higher than they need to be," an EU official said.
Eurotunnel charges a reservation fee of roughly £3,700 (€4,320) to Eurostar for a one-way journey by one of its train, which equates to around £14.15 (€16.60) per passenger. EU officials said the charges should be roughly half that amount.
They added that the tunnel is currently 43 per cent under capacity, largely due to the excessive costs, and if the charges were lowered the company would make up the difference by a doubling of traffic.
Under EU law, rail companies are only allowed to charge fees consistent with the amount of wear caused by a train journey.
But the officials said the Commission investigation found operators of the Channel Tunnel were charging higher-than-necessary access charges, and using this income to subsidise the operator's car shuttle service, which does not pay such charges.
A Eurotunnel spokesman denied the charges were excessive, saying: "Far from preventing growth in traffic, the current regime already enables Eurostar to operate profitably.
"Deutsche Bahn has expressed interest in starting services to Germany and Holland within three years, which indicates other companies are not being deterred by the existing level of charges."