FERGUSON, Mo. — Gov. Jay Nixon ordered the Missouri National Guard to begin a withdrawal from this small city on Thursday, signaling that the authorities believed they had largely restored order after nearly two weeks of unrest set off by the police shooting of an unarmed, 18-year-old black man.

The move came after two nights of calm marked by none of the clashes between the police and protesters that had been a regular occurrence since the Aug. 9 shooting of Michael Brown. In a statement, Mr. Nixon said the situation had “greatly improved with fewer incidents of outside agitators interfering with peaceful protesters and fewer acts of violence.”

In Washington, Attorney General Eric H. Holder Jr., who had ordered a federal civil rights investigation into the shooting soon after it took place, indicated that the federal effort was moving forward. “It’s going to take time for us to develop all the facts, develop all the evidence and see where the case will ultimately go,” he said. “It’s most important that we get it right.”

Federal prosecutors, however, face significant obstacles to bringing civil rights charges in the shooting, officials said Thursday, a reflection of both the unclear nature of the case and the strict standards of federal law.