President Eveline Widmer-Schlumpf, who is also Switzerland's finance minister, said that if Bern and Berlin do not ratify the deal, the existing procedure would continue, whereby Germany would have no option but to launch an independent inquiry for each case of suspected tax evasion.
"No additional steps will be taken to handle requests from Germany," said Widmer-Schlumpf, in an interview with the Swiss newspaper Blick.
Germany should also be aware that a 10-year deadline applies in tax evasion cases, said Widmer-Schlumpf, adding: "In many cases this deadline is nearly up."
Many German tax-dodgers could go unpunished as a result, said Widmer-Schlumpf, asking:"Is that financial justice?"
A tax deal between the two countries, aimed at ending such disputes, is due to take effect on January 1st 2013 but still needs to be ratified by both parliaments.
Widmer-Schlumpf's comments follow talks with German Finance Minister Wolfgang Schäuble on Tuesday in which they discussed the purchase by German authorities of CDs containing details of supposed German tax evaders with accounts in Swiss banks.
According to German media, North Rhine-Westphalia (NRW) purchased a CD that purportedly contained the names of around 1,000 Germans with assets in Switzerland.
Wednesday's edition of Bild indicated that the region had paid a "seven-figure sum" for the CD, its second such purchase.
Schäuble said German regional authorities should refrain from buying such data but Berlin had no power to stop them.
Opposition lawmakers in the German upper house, the Bundesrat, have threatened to block the tax deal.
The two neighbours became embroiled in a major spat in 2010 when German authorities raided branches of Credit Suisse bank in 13 German cities after buying data on suspected tax dodgers.
Between €130 and €180 billion in German assets are hidden in Switzerland, according to German media.