The White House issued a major clarification on Saturday to its new H-1B visa policy that had rattled the tech industry, saying a US$100,000 fee will be a "one-time" payment imposed only on new applicants.

US Commerce Secretary Howard Lutnick, in announcing the major fee increase on Friday, said it would be paid annually, and would apply to people seeking a new visa as well as renewals.

But White House Press Secretary Karoline Leavitt issued a clarification on Saturday, hours before the new policy was to go into effect.

"This is NOT an annual fee. It's a one-time fee that applies... only to new visas, not renewals, and not current visa holders," she said in a social media post.

The executive order, which is likely to face legal challenges, comes into force Sunday at 12:01 am US Eastern time.

Prior to the White House's clarification, US companies were scrambling to figure out the implications for their foreign workers, with several reportedly warning their employees not to leave the country.

"Those who already hold H-1B visas and are currently outside of the country right now will NOT be charged $100,000 to re-enter," Leavitt said.

"H-1B visa holders can leave and re-enter the country to the same extent as they normally would," she added.

H-1B visas allow companies to sponsor foreign workers with specialised skills – such as scientists, engineers, and computer programmers – to work in the United States, initially for three years but extendable to six.

Such visas are widely used by the tech industry. (AFP)