The annual report, the first of its kind, gives a comprehensive view of the scale of incidents, and provides processors with a breakdown of the risks across the food industry.
Food and environmental contamination has been dealt with by the FSA since its formation in 2000, but the authority has only been capable of performing detailed analysis on incidents since the introduction of agency-wide database in 2005.
The incidents, which included the high profile outbreak of Salmonella in chocolate, were largely caused by spills, chemical toxins, pathogens and physical contaminants such as glass, according to the FSA.
The FSA said that although notifications were received from a wide range of organizations, reporting gaps were evident from the data.
Andrew Wadge, FSA chief scientist and director of food safety, said the report stresses the need for cooperation to improve the handling of incidents and encourages more comprehensive reporting.
"A better information base will help us take more appropriate and proportionate action and, over time, provide a valuable resource for everyone concerned with food safety ," he said.
Actions taken by the Agency included 81 food alerts issued to local authorities and 478 notifications to the European Commission, through the Rapid Alert System for Food and Feed.
This system gives Member States two-way intelligence on measures taken to ensure food safety.
Some food incidents that have resulted in product withdrawals or recalls were due to missing or incorrect allergy labelling.
This year, the FSA introduced a SMS messaging service that alerts subscribers to possible allergy risks when they occur.
"This report shows in an accessible way how the FSA responded to the incident reports received in 2006 and highlights how consumer interest was protected, based on that information," Wadge said.
The Agency said the report of 1,342 incidents highlights the need for all food businesses and local authorities to make reporting safety issues a priority.
The FSA anticipates future annual reports of incidents will allow analysis of historical data against the latest statistics to identify trends and provide an accurate picture of food and environmental contamination in the UK.