Toyota is offering its German dealers 7.5 percent but retailers are demanding more than 10 percent.
"The basic margin needs to have two digits," said Burkhard Weller, president of Toyota's German dealers' association.
Toyota wants to keep low sales and distribution costs for the Aygo but says it is willing to discuss ways of helping its dealers.
"We have to rethink the distribution of margins without reducing the level of payment (to dealers) as a whole," said Markus Schrick, managing director of Toyota Germany.
Toyota counts on the Aygo to help it reach its target of 130,000 new-car sales in Germany this year. Its goal is to boost German new-car sales to around 200,000 units by 2010.
The Aygo will be launched across Europe on June 1.