"It would have been fairer and more simple to have a standardized procedure" for dealing with tax evasion, the spokesman, Martin Kotthaus, told a regular government briefing.
"This is what the tax accord signed with Switzerland will do," he added.
Several media have reported that Germany's most-populous region of North Rhine-Westphalia (NRW) purchased a CD that purportedly contains the names of around 1,000 Germans with assets parked in Switzerland.
According to the Financial Times Deutschland, NRW authorities paid about €3.5 million ($4.3 million) for the information.
Kotthaus acknowledged that the purchase of the CD "had not made things easier" in terms of the Swiss tax deal but said it was "decided and carried out in NRW."
According to German media, between €130 billion and €180 billion in German assets are hidden in Switzerland.
A tax deal between the two countries, aimed at ending such disputes, is due to take effect in January 2013 but still needs to be ratified by both parliaments.
"We think this agreement is the right way ... and we are still optimistic that it will be ratified," said Kotthaus.
The double taxation agreement, signed by ministers earlier this year, would see German citizens with assets parked in Switzerland's notoriously secretive banks paying a tax rate of 26.4 per cent on these holdings.
But opposition lawmakers in the German upper house, the Bundesrat, have threatened to block the 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.
Switzerland reacted angrily, saying the data -- bought for a reported €2.5 million -- was stolen in violation of its banking secrecy laws.