The Commission censured the two countries for what it calls "discriminative" low road charges, which it said breached an EU agreement on tolls.
"Both member states apply excessively high discounts of up to 50 per cent and 30 per cent respectively for frequent users of their motorways," the Commission stated yesterday.
Under the Eurovignette Directive, member countries must ensure that road infrastructure charges match the costs associated to the use of this infrastructure..
A recently adopted amending directive specifies that discounts for frequent users may under no circumstances exceed 13 per cent of the toll..
Member states may vary the rates of tolls according to the emission classes of the vehicles using the motorway and according to the time of day. However under the agreement particular discounts for frequent users should not go beyond actual administrative cost savings.
"This provision ensures that all haulers contribute on an equal basis to the cost of the infrastructure they use, and avoids charges below the infrastructure costs for frequent users to be compensated for with higher payments by occasional users," the Commission stated.
It said Spain and France had not provided any evidence that administrative cost savings would justify discounts at the levels which are presently applied.
Earlier this week the Commission published its outline of a common transport policy for the bloc, promising companies supply chain savings and increased efficiency in cross-border trade.
The policy marks a bid by the EU to cut down on pollution, oil consumption and road congestion, mainly by allowing bigger loads and providing designated rail lines between countries for freight.
On average, logistics costs account for 10 per cent to 15 per cent of the final cost of a finished product. The European Commission estimate includes costs such as transportation and warehousing.
Spending on logistics amounts to about €5.4 trillion or 13.8 per cent of the global gross domestic product, GDP a year. Annual logistics expenditure in Europe amounts to about €1 trillion, about the same as in North America, the Commission stated in its policy outline.
The plan includes creating liaisons with member states and industry to deal with bottlenecks in freight transport logistics. There would be a focus on improving the interoperability in countries computer information technologies and communications for better tracking and tracing of goods.
The Commission estimates transport is responsible for 71 per cent of oil consumption and for 26 per cent of CO2 emissions in the EU.
Globalisation of production and the corresponding need for established supply chains increase the need for transportation, the Commission stated in noting the growth of the sector.