The checks, introduced systematically in the last few weeks by the Italians, are "very unpleasant and bad for the image (of Switzerland)", said spokeswoman Veronique Kanel from Suisse Tourisme, the national tourist board.
"The majority (of visitors) are visiting Europe for the first time. Their first impression is very important, and if their experience isn't good, they might think twice about coming back," said Kanel.
Chinese tour operators have also complained about the systematic checks, carried out at the Chiasso customs post.
Their clients are stopped by the busload after visiting the Swiss canton of Ticino, home to Fox Town, one of the biggest shopping outlets in Europe.
If the tourists are found to have purchased items in Switzerland, they are asked to pay an additional 21 percent to bring the items into Italy.
The Italian customs officers "are within their rights to do this", said Kanel, "but it starts to become a problem when big groups are involved".
The 21-percent charge can be reclaimed once the visitors leave Italy to return home, said Kanel: in practice however, their busy schedules and delays in handling their requests mean that they go home empty-handed.
At 350 francs ($360) a day per person Chinese tourists are among the biggest spenders in Switzerland.
Only visitors from the Gulf states spend more, with a budget of 500 francs a day, according to the Federal Office of Statistics.
Michel Bachar, spokesman for Switzerland's Romandie Federal Tax Office, said he was "surprised by the practice, since it involves a massive and unnecessary amount of work".
Visitors were asked to pay the tax on purchases "from time to time" by Swiss customs, Bachar added, "but only when there is a serious doubt about where the merchandise is going".