The arrests came after coordinated raids with Belgian authorities at eight locations across The Netherlands.
"It relates to two managers at the company that allegedly used the substance (fipronil) at poultry farms," spokeswoman Marieke van der Molen said, with Dutch media naming the suspects' company as Chickfriend.
The arrests came after coordinated raids with Belgian authorities at eight locations across The Netherlands with the assistance of Europe's policing and judicial agencies Europol and Eurojust.
"The Dutch investigation focused on the Dutch company that allegedly used fipronil, a Belgian supplier as well as a Dutch company that colluded with the Belgian supplier," prosecutors said.
"They are suspected of putting public health in danger by supplying and using fipronil in pens containing egg-laying chickens," a statement said.
The two men were arrested in central and southern Netherlands in the towns of Barneveld and Zaltbommel.
Police also searched homes in nearby Bergen op Zoom and Uden as well as a storage shed in Ede and two undisclosed locations.
Investigators confiscated paperwork, as well as cars, banking details, and fixed assets.
Dutch prosecutors said they already started a criminal probe in mid-July into how fipronil, which can harm human health, got into the food chain.
The scandal has spread across eight European countries so far with authorities ordering the destruction of millions of eggs and supermarkets in several nations removing eggs from their shelves.
Fipronil is commonly used in veterinary products to get rid of fleas, lice and ticks but it is banned by the EU from being used to treat animals destined for human consumption, such as chickens.
In large quantities, the insecticide is considered by the World Health Organization to be "moderately hazardous" and can have dangerous effects on people's kidneys, liver and thyroid glands.
The problem is believed to stem from a substance used by Chickfriend, that farmers in the Netherlands say they hired to treat their chickens.
A lawyer for a Belgian company, Poultry-Vision, says the firm sold it to Chickfriend but has not said where it got the substance.