The U.S. Federal Aviation Administration on Thursday issued an emergency order prohibiting U.S. operators from flying in an overwater area of Iran-controlled airspace over the Strait of Hormuz and Gulf of Oman due to heightened tensions.

It comes a day after Iran shot down a high-altitude U.S. surveillance drone.

The downing of the unarmed Global Hawk aircraft, which can fly at up to 60,000 ft (18,300 m), was the latest of a series of incidents in the Gulf region, a critical artery for global oil supplies, that included explosive strikes on six oil tankers.

In a separate advisory to operators, FAA said according to flight tracking applications, the nearest civil aircraft was operating within around 45 nautical miles of a U.S. Global Hawk drone when it was shot down by an Iranian surface-to-aire missile this week.

"There were numerous civil aviation aircraft operating in the area at the time of the intercept," FAA said.

The agency said it remained concerned about the escalation of tension and military activity within close proximity to high volume civil aircraft routes as well as Iran's willingness to use long-range missiles in international airspace with little or no warning.

Earlier Thursday, United Airlines said it had suspended flights from New Jersey's Newark airport to the Indian financial capital of Mumbai following a safety review.

"Given current events in Iran, we have conducted a thorough safety and security review of our India service through Iranian airspace and decided to suspend our service," United said on its website, but did not say how long the suspension would last.

Flight tracking data showed commercial aircraft were flying very close to the unpiloted Global Hawk at the time it was shot down, said OPSGROUP, which provides safety guidance to air operators.

"The threat of a civil aircraft shootdown in southern Iran is real," it advised operators on Thursday. "Avoiding the Strait of Hormuz area is recommended — misidentification of aircraft is possible."

Last month, U.S. regulator the Federal Aviation Administration (FAA) advised airlines to exercise caution in flying over Iran and nearby areas, due to heightened military activities and increased political tension.

"Although Iran likely has no intention to target civil aircraft, the presence of multiple long-range, advanced anti-aircraft capable weapons in a tense environment poses a possible risk of miscalculation or misidentification, especially during periods of heightened political tension and rhetoric," it said.

On Thursday, two other carriers, American Airlines and Delta Air Lines, said they did not fly over Iran.

In July 2014, Malaysia Airlines Flight MH17 was shot down by a missile over Ukraine, killing all 298 on board, prompting carriers to take more steps to uncover threats to their planes.

— CNBC contributed to this report.