The men, identified in Dutch media reports as Martin van de B., 31 and Mathijs IJ, 24, briefly appeared before a judge.
The men, identified in Dutch media reports as Martin van de B., 31 and Mathijs IJ, 24, briefly appeared before a judge at the Overijssel District Court in the central Dutch city of Zwolle, in a hearing that was closed to the public.
"The judge decided that there is currently enough suspicion to keep the men in custody," the court said in a statement.
"The public prosecution service suspects the two managers of a disinfection company of using fipronil at poultry farms in the Netherlands," it said.
"Thereby they endangered public health, and there are suspicions they knew that the biocide was banned," the court said.
The two men were arrested Thursday as agents raided eight premises -- including the two men's company, Chickfriend -- in the Netherlands as well as in Belgium.
Dutch farmers and retailers this week began counting the costs stemming from fipronil scandal, which has now affected 17 European countries and stretched as far as Hong Kong.
Initial damages to poultry farms were estimated at at least 150 million euros ($175 million), a spokesman for the ZLTO federation of southern Dutch farmers and gardeners said Monday.
Millions of eggs have been pulled from supermarket shelves and destroyed across Europe and dozens of poultry farms closed since the discovery of contamination with fipronil, which can harm human health, was made public on August 1.
Commonly used to get rid of fleas, lice and ticks from animals, fipronil is banned by the European Union from use in the food industry.
The issue has sparked a row between Belgium, the Netherlands and Germany, the three countries at the centre of the crisis, about how long officials knew about the problem.
Belgium became the first country to officially notify the EU's food safety alert system about the presence of tainted eggs on July 20, followed by the Netherlands and Germany.
The EU insists there is no threat to humans, but the World Health Organization says that when ingested in large quantities fipronil can harm people's kidneys, liver and thyroid glands.