The system, run by the European Commission, provides a means for national regulators to issue alerts to counterparts across the bloc about possible problems in foods and animal feeds.
In total member states issued 3,158 food and feed safety notifications, compared to 2,588 issued in 2004.
The Commission says the rise in food safety incidences may be as a result of more pro-active reporting by member states, improved controls, and an increase in food imports due to enlargement.
The number of notifications has risen steadily each year, indicating that it is becoming more and more established as the first port of call of member states when they detect food safety problems on their markets, the Commission stated.
The system does not name the manufacturers of the products. Meat, poultry and fishery products, fruit and vegetables, and herbs and spices, accounted for the greatest number of notifications.
Among the main hazards notified by national control authorities were the presence of mycotoxins, harmful micro-organisms such as salmonella and e-coli, and illegal substances such as Sudan dyes.
During the year some of the bigger food safety incidents included the discovery of the chemical ITX in liquid baby milk.
The annual report breaks down the overall number of notifications in 2005 into 956 alerts and and 2,202 information notifications.
Alert notifications are sent when the food or feed presenting the risk is on the market and immediate action is required.
About 61 per cent of the alert notifications in 2005 related to products originating in the EU. About 20 per cent of the alerts related to fish and fishery products, 18 per cent to meat and meat products and 11 per cent to herbs and spices.
Information notifications are sent when a risk has been identified but immediate action by other member states is not necessary as the product has not reached their market. This can happen when consignments are stopped at the EU's borders.
About 78 per cent of the information notifications related to products originating in non-EU countries. About one-third of these concerned nuts and nut products.
Overall, 46 per cent of all notifications related to products rejected at the EU border due to the fact that they were deemed to pose a risk to food safety
The alert system also informs the third country from which the product was imported about the problem. In the most serious cases, official letters are sent to the regulators of the exporting countries, who were then expected to follow up with measures such as the delisting of establishments, suspension of exports or an increase in food safety controls.