Although he is dismantling the Obama-era policy allowing new openly transgender recruits to serve in the US military, Trump said in his directive that he will permit the secretaries to use their discretion in deciding how to handle the transgender service members who are already serving.
According to a White House official, transgender individuals can no longer serve in the military unless an alternative decision is made by the secretary of homeland security and the secretary of defense.
President Trump signed a presidential memo Friday instructing the Defense Department to stop accepting transgender people who want to enlist in the military.
In issuing his memo, Trump took aim at the Obama administration, which past year reversed the ban on transgender people openly serving in the US military.
The Obama administration in June 2016 had changed longstanding policy, declaring that troops could serve openly as transgender individuals.
A 2016 Rand Study, commissioned by the Department of Defense and cited by Carter last summer, looked at the effects of integration efforts of foreign militaries and determined "little or no impact on unit cohesion, operational effectiveness, or readiness".
The memo called on Mattis to submit his plan on how to implement the changes by February 21 of next year.
The directive is in-line with his intentions to ban transgender people from serving, as he earlier announced in July. It gives those departments until January 1 to implement the new policy.
The White House offered no guidance at the time as to how the ban would be implemented.
"The President's order to remove transgender service members from the United States armed forces and deny them healthcare is nothing less than a purge", Matt Thorn, executive director of OutServe-SLDN, a group dedicated to LGBT equality in the military, said in a statement.
According to the policy adopted under the Obama administration, commanders have the discretion to decide when to allow transgender troops to start their treatment to transition to a different gender to ensure that it does not disrupt operations.
That is not the military's problem, said Elaine Donnelly, president of the Center for Military Readiness, which has opposed allowing transgender people to serve.
The official would not outline the "factors" that Mattis could use to come up with that policy, leaving open the possibility that some transgender service members could keep their jobs.
Jennifer Levi, an official at Glad, said in a statement "This policy is a shameful slap in the face to people who put their lives on the line everyday to defend our country".