The agency said it is the only category where incidents have consistently increased over time - from 147 in 2006 to 390 in 2014.
Almost a third of resulted from shellfish bed monitoring. High E. coli counts are used to identify poor hygienic conditions in harvesting areas, it added.
Total incidents and causes
The FSA was notified of and investigated 1,645 food, feed and environmental contamination incidents in the UK, which was up from last year.
From next year the agency plans to move to classify incidents by hazard instead of incident type.
The four largest contributors were microbiological contamination (24%), veterinary medicines (13%), environmental contamination (12%) and natural chemical contamination (9%).
Salmonella related incidents dropped to nearer the pre-2011 levels due to a temporary suspension (until 30 June 2015) of imports of paan leaves from Bangladesh and one in 10 of all consignments of paan leaves from India and Thailand had to be sampled and tested until the start of this year.
The frequency of veterinary medicine incidents in 2014 was about five times the average of 2006 to 2012 which reflected a change in reporting procedures.
Fires were the cause of almost four out of every five environmental incidents (79%) and almost all of the remainder referred to spills and leaks or to contamination by heavy metals.
Algal toxins and mycotoxins (mainly aflatoxin) accounted for 87% of natural chemical contamination incidents.
Reported incidents related to unauthorised ingredients rose from 82 in 2013 to 121 in 2014.
The largest increase appears to be related to active ingredients of dietetic supplements. This may reflect making body building products as a 2014/15 sampling priority, said the agency.
Frequency of counterfeit product incidents in 2013 and 2014 is more than three times that of 2006 to 2012.
In 2013 and 2014, more than two-thirds were related to meat, which probably reflects authenticity being a 2014/15 priority in response to horsemeat being found in beef products in 2013.
RASFF notifications
The FSA sent 279 notifications to the European Commission, via the Rapid Alert System for Food and Feed (RASFF).
In total 61% originated within the UK, including almost all the environmental contamination incidents.
Another 9% were related to foods from the rest of the EU, while about 21% were due to imported foods. The origin of the remaining 9% could not be identified.
Reported incidents related to food from more than 50 countries. The EU, China and the US were the biggest contributors from overseas (156, 66 and 65 incidents respectively).
For China, the most common category was food contact materials (26%).
For the US, it was use of unauthorised ingredients (77%), often related to additives in soft drinks and bodybuilding products.
Strategic Plan 2015-2020
Meanwhile, the FSA has published its strategic plan for the next five years.
For food safety it includes a Campylobacter campaign to ensure business delivers less than 10% of whole birds at end of production line with more than 1000 cfu/g.
In its latest results, 19% of chickens tested positive within the highest band of contamination.
Development of a Listeria reduction plan with implementation in 2016-17 is another aim.
The Food Crime Unit, horizon scanning and emerging risks analytical capability and developing proportionate and deterrent sanctions, including work on sentencing guidelines are other areas in the plan.