Health Protection Scotland (HPS) said it had recorded 253 positive cases of E.coli during 2011, up from 212 the previous year.
The agency blamed the increase on a UK-wide outbreak believed to have originated from contaminated vegetables. The outbreak, between December 2010 and July 2011, saw 250 cases of E.coli infection throughout England, Wales and Scotland and 74 victims treated in hospital.
A subsequent investigation pointed to a possible link between leeks and potatoes bought loose and prepared in the home.
However, the HPS report also noted that the apparent spike in E.coli between 2010 and 2011 was partly due to the unusually low rate of E.coli infection in 2010.
The two highest incidence rates among mainland NHS boards were reported by Dumfries & Galloway, which had 13.5 cases per 100,000 population last year, and Grampian, where it was 7.8 per 100,000 compared to the national average of 4.8 per 100,000.
The report also noted decreases in salmonella and campylobacter.
In 2011, HPS received reports of 736 cases of salmonella infection – a decrease of almost 22% on the 941 reported in 2010.
Cases of campylobacter were also down 3.6% to 6366 last year, although the figure remains "one of the highest on record".