In addition to Suzuki managers, executives at Fiat Chrysler (now Stellantis) and Marelli are also under suspicion, the dpa news agency reported.
The engines were allegedly delivered by Fiat Chrysler and the software allegedly was provided by Marelli.
On Wednesday, business premises of the companies involved in Heidelberg, Germany, Corbetta, Italy and Esztergom, Hungary, were searched. Prosecutors seized communication data, software and planning documents, dpa said.
The searches part of a coordinated action by Eurojust, Europe's agency for criminal justice cooperation.
"The devices were allegedly fitted in the Italian-built diesel engines of large numbers of cars, giving the impression that the vehicles' nitrogen oxide emissions were in line with EU regulations," the agency said.
The engines were assembled into the cars in Hungary, where Suzuki has a plant, the agency added.
Suzuki formed an alliance with Fiat to make diesel engines in Asia in 2005. It expanded the agreement to buy engines from Fiat in Hungary in 2011.
A spokesperson Suzuki, whose European headquarters are in Germany, said the company and local management "are cooperating with the investigating authorities."
Stellantis said its subsidiary FCA Italy had been asked as part of an investigation in Frankfurt to provide information and documents "regarding the use of allegedly impermissible emissions control software in diesel engines supplied to Suzuki."
"The company will continue to fully cooperate to investigations in this matter," the carmaker said in a statement
Marelli said in a statement that it was cooperating with investigators. "Marelli is confident that we have always conducted our operations in full compliance with regulations," it said.
Regulators across the world have been testing diesel models since Volkswagen Group admitted in 2015 that it used illegal software to cheat U.S. emissions tests.
VW admitted to using the software to rig diesel engine tests and said that 11 million vehicles worldwide were involved. So far, the scandal has cost the German automaker more than $40 billion in vehicle refits, fines and provisions for future legal claims.
Reuters contributed to this report