Morgan told employees on a phone call Thursday morning that he was not resigning but had been asked to leave by the Trump administration, said a Department of Homeland Security official who spoke on the condition of anonymity.
Morgan's departure comes one day after President Donald Trump announced a broad plan to crack down on border security, including directing the construction of a wall along the border with Mexico.
The border patrol union, which endorsed Trump's presidential campaign and applauded his executive order, had been critical of Morgan. The union criticized Morgan for supporting former President Barack Obama's plans to safeguard certain undocumented immigrants from deportation.
The executive board of the National Border Patrol Council called Morgan arrogant and a "disgrace to the Border Patrol" in an opinion piece published by conservative website Breitbart News on Nov. 30.
Unlike many border patrol officers, Morgan did not climb the chain of command within the agency but was appointed from the FBI.
Banner and thumbnail credit: Reuters, Jorge Duenes