The FAA has issued an emergency flight restriction prohibiting civilian aircraft from entering the airspace over Iraq, Iran and the waters of the Persian Gulf and Gulf of Oman.
In the last hour the US aviation body issued a Notice to Airmen or "Notams" to US-registered operators.
Issuing the three separate Notams "banning" flights over Iran, Iraq and the surrounding airspace, the FAA said it was :
"Due to heightened military activities and increased political tensions in the middle east, which represent an inadvertent risk to US civil aviation operations due to the potential for miscalculations or misidentification."
The US Federal Aviation Administration said it would "continue closely monitoring events in the Middle East. We continue coordinating with our national security partners and sharing information with US air carriers and foreign civil aviation authorities."
The Notams come approximately four hours after Iran launched missile attacks into at least two US airbases inside Iraq.
While the exact scale of the attack is still unclear – with the Iranian Revolutionary Guard claiming the attack involved "tens of missiles" across the border – the aviation body decided to issue the warning to avoid affected airspace.
While the notice only applies to US registered operations, other airlines and international aviation bodies have taken similar moves to avoid the potentially hazardous airspace.
According to The Straits Times Singapore Airlines has diverted all aircraft around the implicated airspace.
The potential for misidentification is a concern for passenger airlines. In 1988 during the Iran-Iraq war a civilian airliner was shot down over the Strait of Hormuz by the US Navy.
Iran Air flight 665 was misidentified as a cruise missile by the USS Vincennes which shot down the plane, killing all 274 passengers and 16 crew on board.
More recently Malaysia Airlines Flight MH17 was downed over the Ukraine by a surface to air missile in 2014, killing 298.
On Tuesday IATA and the International Civil Aviation Organization (ICAO) activated a warning over the Gulf area as a "standard precautionary measure," in the event that contingency measures are required by airlines, according to Reuters.
The area is home to a very busy air corridor for commercial and civilian air traffic, with some of the world's largest international air hubs serving the route out of Dubai and Qatar.
During the exchange of missiles from Iran, state TV reported that a Ukrainian International Airlines plane carrying 180 passengers crashed on the outskirts of Tehran.
It is not clear if the Boeing 737 crash is connected to the Iranian missile strikes.