Trump signed a proclamation in September that imposed the new fee on the program, which has been the target of immigration hawks for years. Critics have argued large firms use the program to import cheap labor, mostly from India, to replace Americans.
The department said the change includes international students and temporary workers, stating those who are in the U.S. on temporary visas are expected to only remain in the country for a set time.
The change is likely to affect hundreds of thousands of people. It could also lead to more family separations as spouses or relatives wait for application decisions, immigration lawyers said.
U.S. Rep. Beth Van Duyne, R-TX, and her north Texas colleagues have called for a federal investigation into alleged H-1B visa fraud occurring in counties they represent.
Restaurant operators say labor shortages, rising costs and worker fear have prompted an unusual alliance of industry and political leaders in Texas to call for legal pathways to hire immigrants.