The tax inspectors, all from North Rhine-Westphalia, are wanted for “economic espionage,” Swiss prosecutors confirmed on Sunday.
Arrest warrants have been issued on the trio in the latest development in a long-running spat between the two countries.
“There's concrete reason to suspect Germany of having given clear orders to spy on Credit Suisse information” Swiss prosecutor Michael Lauber told Swiss radio station DRS on Saturday.
German regional authorities, however, said the inspectors had done "their duty" by pursuing German tax evaders who were hiding money in Swiss bank accounts.
“The real criminals are not our tax inspectors, but those in Germany who exploit the conditions in Germany to accumulate massive profits then disappear into the dust and leave the payments to the honest tax payers,“ said North Rhine-Westphalia state Finance Minister Norbert Walter-Borjans on Saturday.
“The criminals also include those who have made assisting tax evasion their business model,” he added.
In 2010, the Düsseldorf prosecutor's office raided branches of Switzerland's second biggest bank in 13 German cities as part a probe of 1,100 clients and bank staff suspected of hiding funds from tax officials.
The raid came after officials in the German state of North Rhine-Westphalia paid a reported €2.5 million for a computer disc containing information on wealthy Germans linked to the investigation.
This weekend's latest spat comes as a proposal to make German investors in Switzerland pay the same amount of tax as they do at home seems on the edge of collapse due to renewed resistance from the German opposition.