US President Donald Trump on Wednesday issued an executive order directing Secretary of State Marco Rubio to revamp the foreign service to ensure "faithful and effective implementation" of Trump's foreign policy agenda.

The order, which follows upheaval at the US Agency for International Development, comes as Trump institutes changes to ensure US foreign policy is aligned with his "America First" agenda. He has also repeatedly pledged to "clean out the deep state" by firing bureaucrats that he deems disloyal.

The order also says failure to implement the president's agenda is grounds for professional discipline, which may result in the termination of personnel.

"The Secretary must maintain an exceptional workforce of patriots to implement this policy effectively," the order read.

"The Secretary shall, consistent with applicable law, reform the Foreign Service and the administration of foreign relations to ensure faithful and effective implementation of the President’s foreign policy agenda."

The executive order says the secretary of state will implement reforms in recruiting, performance, evaluation and retention standards to "ensure a workforce that is committed to faithful implementation of the President’s foreign policy."

It also said the secretary can revamp the programs of the Foreign Service Institute and revise or replace the Foreign Affairs Manual.

Just hours after taking office on January 20, Trump ordered a freeze of most U.S. foreign aid to ensure it was aligned with his "America First" policies.

Following the order, USAID staff were put on leave and told not to report to work at the agency's headquarters, where signs were covered in tape or removed. The USAID website stopped working and Secretary of State Marco Rubio was named acting administrator.

Current and former USAID officials told Reuters that the purge of some senior staff at the agency appeared designed to silence any dissent.