The US Congress is debating whether to introduce a $10 tax on the so-called Electronic System for Travel Authorization (ESTA) and channel the money back into the US tourism industry.
"Our position is that if such a tax is introduced, that will obviously lead the (European) Commission to re-evaluate the ESTA," said a justice affairs spokesman at the EU's executive body.
"It is clear that this could represent a step backwards in our efforts to improve transatlantic mobility," he said.
Since January 12, travellers from 35 countries have been obliged to request authorisation online to enter the US.
The ESTA systems applies to largely European countries plus Australia, Brunei, Japan, New Zealand, Singapore and South Korea.
These countries are exempt from visa requirements to enter the United States for short visits under the US Visa Waiver Program (VWP).
Before the system was introduced, the commission said it was satisfied the ESTA was not a visa in disguise, although officials did express reservations about whether that would still be the case if the document had to be paid for.
South Africa is not part of the VWP, and South African-passport holders require a visa to visit the USA.
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