"To the Senate of the United States. I withdraw the nomination of Ronald D. Vitiello, of Illinois, to be an Asistansten Secretary of Homeland Security, vice Sarah R. Saldana, which was sent to the Senate on January 16, 2016", Trump said in the letter dated 4 April and obtained by CNN on Friday.
The president did not disclose his reason for pulling Vitiello's nomination.
The move caused confusion within the Department of Homeland Security, with some officials initially calling it an error, according to media reports.
The news comes amid the ongoing disagreement over US border security between Republicans and Democrats.
Trump, who described the situation at the country's southern border with Mexico as a crisis, said on Thursday that Mexico is could face a potential 25 percent tariff on its car imports to the United States if it does not do enough to stop illegal migration and drug trafficking.
Mexican President Andres Manuel Lopez Obrador has said that neither Washington nor Mexico City would benefit from a closure of the border.
According to Mexico’s Ministry of Internal Affairs, more than 76,000 migrants were detained after trying to get into the United States in February, while in March the figure was expected to increase to 100,000 people.