The proposed fee, up from the current $2,000-10,000 cost per petition, is expected to affect on-site hiring by Indian IT firms and could encourage US enterprises to shift more work offshore
The Labour Department's watchdog says it is investigating alleged abuse of foreign worker visa programmes, including claims of fraudulent applications and worker exploitation.
District Judge Leo Sorokin in Boston ruled that the fee, announced by Trump in September last year, was an unlawful tax that the President did not have authorisation from Congress to issue.
Senator Susan Collins argued that healthcare providers in underserved regions should be treated differently from employers hiring skilled workers in sectors with larger domestic talent pools.
The pause in the red state, which is home to thousands of H-1B visa holders, comes amid actions by the Trump administration aimed at reshaping the visa program.