"Samples analysed in the Netherlands show traces of fipronil in the eggs, but not as a health hazard", the agency said.
With concern going global, the commission said it had now called a meeting of ministers and food safety chiefs from affected European Union countries, setting a provisional date of September 26.
The Foods Standards Agency said 700,000 eggs had been sent to the United Kingdom from potentially contaminated Dutch farms.
EU Trade and Agriculture spokesman Daniel Rosario said on Friday that farms were shut down in the Netherlands, Belgium, Germany and France after authorities confirmed that fipronil had been used.
The EU countries which received the contaminated eggs included UK, Sweden, Austria, Ireland, Italy, Luxembourg, Poland, Romania, Slovenia, Slovakia and Denmark.
The consumption of eggs tainted with Fipronil, often used to kill lice and fleas, poses low risks to public health, according to the World Health Organisation.
But the insecticide can damage people's kidneys and livers if eaten in large quantities.
Here's how you can see the Perseid Meteor Shower Saturday night
At its peak, the Perseid meteor shower will see about 50-60 meteors from the Swift-Tuttle comet cruise across the sky every hour. This biggest meteor shower of the year is going on this weekend, and Saturday night is the most optimal time to see it.
"The Centre for Food Safety is now inspecting eggs coming from Europe closely, no matter at the import, or at the retail level", Chan said.
A spokeswoman in Brussels said the situation was "evolving by the day", as criminal investigators continued to hold two men arrested for fraud after a series of raids in Belgium and the Netherlands.
But across the border here in Germany supermarkets have withdrawn millions of eggs from sale while in Belgium and the Netherlands have also taken off millions of eggs from their shelves.
Egg imports are stringently controlled and only those with recognized health certificates can be imported to Hong Kong, she added.
"Food safety is Wellcome's first priority".
"Customers can bring the product along with the receipt to the store for either a merchandise exchange or refund when they have queries about the products purchased", he added.