"Millions of people were affected and little information is a recipe for fear, rumours and anger."
Read more: Lettuce food poisoning: 'Everyone wants a scapegoat'
The contentious Ruataniwha Dam project and rate increases by Auckland Council also made the top three challenges.
Notable PR failures this year included David Cunliffe's apology for being a man, the State Services Commission's press conference with Roger Sutton and Kim Dotcom's failure to deliver his "Moment of Truth" about John Key, Mr Blackham said.
Media commentator Bill Ralston described the handling of the Roger Sutton sexual harassment allegations as a "major PR stuff up".
"It's done him enormous damage, regardless of whatever might have happened to prior that occasion, it should have been handled so much better than it was.
"Roger should never have gone in there," Ralston said.
"I think the biggest PR failure is Kim Dotcom ... it's demonstrable ... the man just did a faceplant with his otherwise quite interesting story.
"If he'd under-sold it, it might have had more impact than his over-selling and the unfortunate email that wasn't really a leaked email that showed collusion and bad faith on the part of the US film companies."
The best PR went unseen or occurred when an organisation's message coincided with the values of the average kiwi, Ralston said.
"That's when it works," he said.
"You're best when you just say something that hits a nerve, it might be as simple as Andrew Little saying 'cut the crap' - sometimes just a short soundbite phrase will do it for you."
Damage control PR needed to include public concern for anyone that had been injured or damaged - including an apology if necessary, the show of a form of action and perspective, Ralston said.
BlacklandPR spokesman John Mitchell said hundreds of possible PR challenges were considered before the top 20 were selected.
The challenges were measured on their direct and indirect impacts, their profile in the media, the intensity of emotional reaction, and their complexity.
"Roger Sutton didn't have a high impact because those affected by it were essentially Ian Rennie, Roger Sutton and the complainant in the case, whereas you have a situation like the dirty lettuce and carrots for example - a whole lot of people were impacted by that because of the uncertainty."
Mr Blackham said it was interesting to see some previously contentious issues lose their emotive power over time, such as the outcome of the police Roastbusters investigation and Solid Energy's decision not to re-enter the Pike River mine.
"Despite previous attention, the return of these issues was only on the public agenda for less than 24 hours," he said.
Top 20 toughest PR issues of 2014:
1. Carrots and lettuce food poisoning issue, Ministry for Primary Industries
2. Ruataniwha Dam, Hawke's Bay Regional Council
3. Auckland rates, Auckland Council
4. Christchurch flooding, Christchurch Council
5. Ashburton shooting, Work and Income
6. William and Kate Royal visit, Department of Internal Affairs
7. Regional flight closures, Air New Zealand
8. Roast Busters prosecution decision, Police
9. Dirty Politics, National Government
10. Phillip Smith's escape, Corrections
11. Malaysian diplomat, Ministry of Foreign Affairs and Trade
12. Pike River re-entry, Solid Energy
13. Ebola preparations, Ministry of Health
14. Match-fixing allegations, New Zealand Cricket
15. Shane Jones' supermarket exterortion allegations, Foodstuffs
16. Roger Sutton's resignation, State Services Commission
17. New currency, Reserve Bank of New Zealand
18. Chocolate milk, Lewis Road Creamery
19. Telecom's rebranding, Spark
20. Carterton hot air balloon report, Transport Accident Investigation Commission