While Berlin puts the total at 10.7 million eggs, the agriculture minister of the state of Lower Saxony said that 35 million possibly tainted eggs had made it to his state alone from the Netherlands.
The state minister, Christian Meyer of the ecologist Greens party, accused Berlin of "playing down the problem" and said his figures were backed by EU data.
At the national level, a spokeswoman for Agriculture Minister Christian Schmidt of the conservative CSU party denied the claim and accused Meyer of politicising the issue ahead of a national vote on September 24th and a state poll in October.
"One shouldn't use consumer fears for election campaigns," said Schmidt's spokeswoman, Christina Wendt.
Fipronil is commonly used to get rid of fleas, lice and ticks from animals but is banned in the European Union from use in the food industry.
The insecticide has now been discovered in eggs in 17 European countries since the scandal came to light at the start of August and was even found as far away as Hong Kong.
Millions of eggs have been pulled from supermarket shelves and dozens of poultry farms closed, with the European Commission due to hold a crisis meeting in September.
Belgium became the first country to officially notify the EU's food safety alert system of the presence of tainted eggs on July 20th, followed by the Netherlands and Germany.
However, the news did not go public until August 1th.
The EU insists there is no threat to humans, but the World Health Organization says that when eaten in large quantities it can harm people's kidneys, liver and thyroid glands.