At least 21 embassy staff and family members reported a range of health problems including deafness, dizziness and nausea to mild brain trauma.
Earlier reports said Washington made the order after diplomats were targeted by sonic attacks, which use sonic and ultrasonic weapons to injure, incapacity or kill an opponent.
Citizens were urged not to travel to Havana because some of the attacks took place at hotels were Americans stay, according to a senior State Department official.
American officials said the US embassy will lose around 60 per cent of its staff, and will stop processing visas there indefinitely.
A US state department official said: “Until the government of Cuba can ensure safety of our people, we will be reduced to emergency personnel so as to minimise the number of US government personnel at risk of exposure.
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“Routine visa operations are suspended indefinitely.
“At least 21 employees have been targeted in specific attacks.”
He said non-essential embassy staff would be withdrawn as well as all family members.
The Cuban government has denied any role and is investigating the incident.
Despite an investigation by the FBI, Cuban authorities and the Royal Canadian Mounted Police, officials have been unable to determine the cause of the attacks, which date back to late 2016.
But the senior State Department official stressed “the government of Cuba is responsible for taking all appropriate steps to prevent attacks on our diplomatic personnel in Cuba”.
The official said: “We don’t know the means, the methods or how the attacks are being carried out.”
The partial evacuation is set to deliver another blow to former US President Barack Obama’s policies of engagement with Cold War foe Cuba.
Although Washington has not cast direct blame on Cuban authorities, Secretary of State Rex Tillerson reminded Cuban Foreign Minister Bruno Rodriguez that it was Cuba’s obligation to protect diplomats and their families during a meeting in Washington on Tuesday.
The symptoms of the 21 US embassy personnel harmed included “hearing loss, dizziness, tinnitus, balance problems, visual complaints, headache, fatigue, cognitive issues and difficulty sleeping”.
Denis Bedat, a specialist in bio-electromagnetics, earlier this week said staff in Havana could have been targeted by audio-waves, which left them with chronic hearing issues.
Mr Bedat said using an inaudible sound device for a sonic attack is “quite plausible from technical point of view”.
He added: “Ultrasonic waves, beyond the acoustic capacity of humans, can be broadcast with an amplifier and the device does not need to be large, or used inside or outside the house.”
The senior State Department official added: “Because our personnel’s safety is at risk and we are unable to identify the source of the attack, we believe that U.S. citizens may also be at risk and warn them not to travel to Cuba.”