The proposal, which is expected to be published at the end of May, will also include buses and coaches as well as a requirement for motorists to pay according to the distance travelled.
The proposal will keep the average level of tolls collected roughly constant, meaning more polluting vehicles will pay more while cleaner ones will pay less.
The EU currently has a legal framework governing toll charges for trucks, but road tolls for private vehicles are left to national governments.
The proposal will not force countries to introduce road charging schemes for cars or trucks, but will lay down rules any such scheme would have to respect were it to be introduced.
The proposals will need the approval of the European Parliament and of member states before they can be implemented.