Another US patrol craft and a Kuwaiti Navy ship were also harassed in the incident, which took place in the northern end of the Persian Gulf on Wednesday, CNN reported.
At one point, the Iranian boat came within 200 yards of one of the US Navy boats.
When it failed to leave the area after the Navy had fired flares and had a radio conversation with the Iranian crew, CNN quoted the US officials as saying.
The USS Squall fired three warning shots.
Following standard maritime procedures, the Navy fired the three shots into the water to ensure the Iranians understood they needed to leave the immediate area.
State Department spokeswoman Elizabeth Trudeau said incidents like this one "unnecessarily escalate tensions" adding that the US does not know Iran's intentions.
In an encounter on Tuesday, a US Navy official told CNN that four Iranian Revolutionary Guard Corps vessels conducted a "high-speed intercept" of the USS Nitze in waters near the Strait of Hormuz, deeming the incident "unsafe and unprofessional".
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