The posts came in response to moves being reportedly made by the Doge - which is not a government department, but a team within the administration.
The team has been given the job of radically reducing regulation and federal government spending.
US media has reported the Trump administration gave Musk's deputies access to the federal payments system that controls the flow of trillions of dollars in government funds every year.
It has led to backlash online with people criticising the decision, and the names of the Doge staff involved being shared publicly.
But the decision to remove the subreddit may have been about more than Reddit enforcing its policies.
On Monday, a prosecutor appointed by Trump said the FBI was investigating the "targeting" of Doge staff.
"Our initial review of the evidence presented to us indicates that certain individuals and/or groups have committed acts that appear to violate the law in targeting Doge employees," said United States Attorney for the District of Columbia Edward Martin.
In a letter to Musk he posted on X, Mr Martin said he would "not tolerate threats against Does workers or law-breaking by the disgruntled".
"Any threats, confrontations, or other actions in any way that impact their work may break numerous laws," he wrote.
"We will pursue any and all legal action against anyone who impedes your work or threatens your people."
