The frontrunner to become Britain's next prime minister used the kipper to emphasise why his country should leave the European Union as soon as possible.
Addressing members of his ruling Conservative party at a London rally on Wednesday, he said the fish came from "a kipper smoker in the Isle of Man who is utterly furious".
"Because after decades of sending kippers like this through the post, he has had his costs massively increased by Brussels bureaucrats, who have insisted that each kipper must be accompanied by this -- a plastic ice pillow," he said, holding that up too.
But Anca Paduraru, the EU Commission's spokeswoman for food safety and health, rejected this at a Brussels briefing on Thursday.
While the producer had a duty to meet food safety requirements, she said "the sale of products from the food business to the final consumer is not covered by EU legislation on hygiene".
She added: "There are strict rules when it comes to fresh fish but these kinds of rules don't apply to processed fishery products -- I'm talking about the temperature and the exact case that he was explaining."
Kippers are whole fish, normally herring, which are split from head to tail, gutted, salted and smoked.
"So this means that the case described by Mr Johnson falls outside the scope of the EU legislation and it's purely a UK national competence," Paduraru said.
- Isle of Man law -
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However, a spokeswoman for the Isle of Man government told AFP the rules on keeping kippers at the right temperature date back to 2007 legislation passed there.
It was introduced a few months after new EU regulation on the topic.
The Isle of Man is not a member of the EU but as a self-governing British Crown Dependency, has access to the bloc's customs union which allows the movement of industrial and agricultural goods.
As a result, it must apply certain EU regulations, while it also keeps step with laws in Britain, its largest trading market.
The spokeswoman said she was "delighted to see such interest in our world renowned kippers".
"The Isle of Man law is closely based on UK legislation and relevant EU food safety regulations," she said.
"Where our goods are exported they are required to comply with standards of the destination market."
Britain's Food Standards Agency said that in the UK all food delivered to customers that needs refrigeration "must be kept cool while they are being transported".
"This may need to be packed in an insulated box with a coolant gel or in a cool bag," it said.
A kipper producer on the Isle of Man, who said they did not provide the fish used by Johnson, confirmed they had received new advice on how to store the fish.
But an official indicated this was probably the result of efforts to reinforce the current rules, as the country prepares for any disruption from Brexit.
Before he entered politics, Johnson made his name as a journalist in Brussels writing about absurd EU regulations, which drew accusations of exaggeration.
The likelihood that he will replace Theresa May as Britain's prime minister next week, charged with taking his country out of the bloc, has alarmed many in Brussels.
EU Health Commissioner Vytenis Andriukaitis accused Johnson of "fake news".
"Boris, the Isle of Man is not bound to the #EU 'pointless and damaging' *red tape* in #foodsafety that we are proud of because it protects consumers," he tweeted.
"You omitted to say that the Isle of Man is not in the EU. This packaging -- #uk competence. Yet another smoke. #fakenews".