In one of a number of dangerous events listed by the Federal Aviation Administration, a US civil operator was intercepted by fighter jets in the skies above Iran last December.
The advisory also warns military activities linked to the bloody conflict in Syria have been ramped across Iran’s airspace.
Tensions between Tehran and Washington are running high following Donald Trump’s controversial decision to pull out of the landmark Iran nuclear deal re-introduce economic sanctions last month.
Flight Service Bureau, which provides safety information on airspace to airlines, said “without seeming alarmist”, the deteriorating relationship between the US and Iran must be taken into account when planning flights in Iran’s airspace.
In an email to client operators the US-based group said: “Although the reopening of Iraqi airspace in November last year has provided additional routing options, there is no perfect route in the region, and operators must consider their preference for Iraq vs Iran.”
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The US Department of State has already issued guidance advising its citizens not to travel to Iran due to the risk of arbitrary arrest and detention.
Flight Service Bureau said that could present problems in the event of an unplanned landing in Iran for medical or technical reasons.
Similar advice is issued for travel to Iraq, amid the risk of terrorism and armed conflict.
The FAA’s latest guidance on Iraq, issued in December 2017, prohibits US airlines in most cases from flying at an altitude lower than 26,000 feet due to the potential for fighting.
Iran’s nuclear chief said he hoped the atomic deal between Tehran and world powers could survive Washington’s withdrawal but warned his country’s nuclear programme would be in a stronger position than ever if not.
The remarks by Ali Akbar Salehi, who also serves as a vice president to Iran’s elected leader Hassan Rouhani, come as Iran tries to salvage the accord.
Mr Trump’s decision to walk away from the deal and the return of US sanctions has already rocked Iran’s fragile economy and crashed its rial currency.
Further sanctions coming in November threaten Iran’s oil industry, a major source of government funding and will put further pressure on the relatively moderate Mr Rouhani.
Mr Salehi sought to contrast Iran’s behaviour, which includes abiding by the atomic accord, against “emotional moves and sensational moves.”
He said: ”I think Trump is on the loser’s side because he is pursuing the logic of power.
“He thinks that he can, you know, continue for some time but certainly I do not think he will benefit from this withdrawal, certainly not.”