The agreement paves the way for paperless transactions. It also targets simplifying current legislation and streamlining customs process and procedures for traders.
The new agreement now needs to be confirmed by the European Parliament in a second reading, expected to come in the next few months. The new code is expected to become law by early next year.
"In full respect with our better regulation and e-government strategies, the modernised Community Customs Code will provide fewer and simpler rules adapted to a modern electronic and paperless customs environment," said László Kovács, the EU commissioner responsible for taxation and customs.
Currently all 27 member states have electronic customs systems, but these are mostly not inter-connected. The new agreement would require governments to make their electronic customs systems compatible with each other.
A single, shared computer portal would be created for the bloc. Electronic declarations would become compulsory, with paper-based declarations becoming the exception.
Authorised traders will also have access to a centralised clearance scheme, under which they will be able to declare goods electronically and pay their customs duties at the place where they are established, regardless of the member state through which the goods will be brought in or out of the EU customs territory or in which they will be consumed.
The new cross-border Automated Import System and Automated Export System as it is being called would be linked with the EU's existing computerised transit system.
The network would ease the customs procedures relating to export, import and transport, avoiding duplication at the EU level, the Commission stated.
The systems would ensure that import and export operations started in one EU member could be completed in another without companies having to re-submit the same information.
Through a new EU customs portal, traders would deal with one regulatory body instead of several frontier control authorities as happens at present.
The system would then allow goods to be controlled by customs and other authorities - including veterinary, sanitary, food safety and environmental inspectors - at the same time and at the same place.
Business would also be assigned a unique identification for customs purposes.
Ireland in particular has welcomed the decision to cut the red tape.
The country's minister for enterprise, trade and employment, Micheál Martin, said the decision was significant in helping to cut costs for exporters.
"The new set of rules, the Community Customs Code, means that Irish exporters will no longer have to engage customs agents in the country they are exporting to," he said yesterday.
About 64 per cent of Irish exports are sent to other EU countries.
In 2005, exports inside the EU reached €146.4 billion. This amount is considerably higher than the extra-EU sales.
The intra-EU exports account for 17.5 per cent of the turnover in 2005. At the same time, trade to non-EU countries accounted for 5.7 per cent of the turnover.