The decision was made after an incident involving an audio device, a senior US Department of State official told reporters on Friday.
"On September 29, the [State] Department ordered the departure of non-emergency personnel assigned to the US embassy in Havana as well as all family members," the official said. "Until the government of Cuba to ensure the safety of US government personnel in Cuba, our embassy will be reduced to emergency personnel."
The United States does not eliminate the possibility of a third country being involved in sonic attacks against US diplomats in Cuba, the official added.
"We have not ruled out the possibility of a third country as a part of the investigation, but that investigation continues," the official stated.
The official added US investigators do not know the methods, the means or how the sonic attacks were carried out.
The last report of attacks was received in August, the official noted. Meanwhile, the State Department has not confirmed that the incidents have completely stopped.
The Cuban government is cooperating with the United States in the ongoing investigation into the incidents, the official said.
The United States is suspending issuing visas in Cuba, the official told reporters.
"Routine visa operations are suspended indefinitely," the official said.
Previously the US media reported the US was planning to withdraw most of its diplomats from Cuban capital of Havana after embassy workers allegedly suffered brain injuries caused by sonic weapons.
In August, US State Department spokeswoman Heather Nauert said diplomatic personnel working in the US embassy in Cuba were involved in an incident that resulted in physical symptoms. The investigation into injuries of US diplomats allegedly sustained in Havana had not found any evidence that ccould confirm the injuries' origin.
The incidents, allegedly caused by a sonic weapon, have affected at least 21 diplomats, some of whom appear to have suffered permanent hearing loss and possibly brain injury, according to media reports.
On September 14, US senators sent a letter to State Secretary Rex Tillerson, urging the State Department to close the embassy in Havana and expel all Cuban diplomats from the United States, since Cuban authorities failed to ensure the security of US diplomats.
Last week, Tillerson told CBS that the US government was considering closing its embassy in Cuba. On Thursday, a meeting between Cuban Foreign Minister Bruno Rodriguez and Tillerson took place in Washington. The talks between the two diplomats focused on ensuring the safety of US diplomatic staff.