Stephan Moelans, the CEO of Sabcobel, which operates Delhaize's systems, on Monday told the Belga news agency that the incident was a cyber-attack and that the company had been "working all night and morning to disconnect the affected units from the network".
He said since the French attack in early October, the company had been working to "protect our customers fridges against this vulnerability" but that the units needed physical modifications, not just software updates.
Most supermarkets across Europe are linked to the internet, and maintenance and troubleshooting can be done remotely.
"The simplest solution is to manage the fridges over a secure internet connection. Most of our customers switched to that after the attack in France," Moelans added.
The temperature of freezers in several shops across Europe reportedly rose to as high as 50C (122F).
It is unclear who is behind the latest apparent attack.
In the US, authorities are investigating what caused refrigeration malfunctions at a number of American military bases in August and working together with French officials to examine whether the incidents could be linked.
Both Belgium and Sweden's national cyber-security agencies said they were monitoring the incident.
The UK's National Cyber Security Centre said it was working with international partners and industry to "fully understand details of an incident". No incidents have been reported in the UK.
In Flanders, northern Belgium, a Delhaize branch in Hoeilaart told news website Het Laatste Nieuws it had lost €100,000 (£83,500) worth of produce.
The manager said that estimate did not even take into account further losses that would result from closing the shop.
Carrefour, a French-owned supermarket, said the incident had only affected 15 of its Belgian stores, adding that measures had been taken immediately to ensure all shops remained open.
A spokesperson for Colruyt Group, which operates Spar stores in Belgium under a franchise system, told Reuters news agency five shops had their fridge systems attacked.
Sweden's budget furniture retailer Ikea said refrigeration systems of its store in the western Belgian city of Mons were affected, with a spokesman quoted by Reuters as saying "we cannot rule out that additional locations may be affected".
In Sweden, several ICA and Coop shops were hit.
A spokesperson for ICA confirmed the incident had affected a "small number of ICA stores operating outside ICA's central network".
"ICA is currently supporting the affected stores in managing the situation," they said.
One of the ICA branches located in Sjöbo, southern Sweden, wrote on social media: "Our refrigerators and freezers have been hacked overnight and they have set the temperature to 50 degrees."
The store was closed earlier but has now reopened to customers.
Seven out of the 800 Coop stores in Sweden were also affected but the "situation is currently contained and under control", the company told the BBC.
In neighbouring Finland, refrigerator malfunctions were detected in some K-stores.
The owner of the supermarket chain Kesko was quoted by Finland's Helsingin Sanomat newspaper as saying its security experts were investigating what caused the problem.
The attack is also affecting shops in Ireland, the Netherlands and Estonia.
In Ireland, it impacted 13 SuperValu supermarkets. A spokesman for the owner of the chain, Musgrave Group, confirmed to The Irish Times that a "cyber incident" affected its refrigeration systems, but added that the impact was limited to a "specific model" of refrigerator.
A spokesperson for Danish manufacturer Danfoss told Dutch public radio channel NOS that the freezing and cooling systems of at least 17 companies in the Netherlands were attacked overnight, affecting butcher shops and small neighbourhood stores.
A Selver supermarket in Estonia was also affected and there are reports of other affected companies in the country, according to ERR.
Additional reporting by Shiona McCallum
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