Since taking office, Mr Trump has twice signed executive orders banning refugees and citizens from some Muslim-majority countries from visiting the United States. Although both moves were blocked by US judges, some travellers have been deterred.
The US administration also introduced new security measures in March banning electronic devices larger than a mobile phone from being taking into aircraft cabins on direct flights to the United States from several Middle East locations.
"The recent actions taken by the US government relating to the issuance of entry visas, heightened security vetting and restrictions on electronic devices in aircraft cabins have had a direct impact on consumer interest and demand for air travel into the US," an Emirates spokeswoman said.
Detailing changes to flight schedules, she said, "This is a commercial decision in response to weakened travel demand to the US"
Twice daily Los Angeles flights would also be reduced in July to one a day, it added.
(Reporting by Alexander Cornwell, Editing by Edmund Blair)