Addressing a news conference on Wednesday, the spokesman said there were no plans to pull EU officials out of Iran or Iraq.
Canada, which leads the NATO training mission, said it was pulling out some of its 500 troops, and Germany said its presence in Iraq would be “temporarily thinned out.”
German soldiers are stationed at the Irbil air base and Berlin has pulled some of its military personnel out of Iraq citing security concerns.
Most of the withdrawing NATO troops were reported to be heading for Kuwait.
The US Federal Aviation Administration has barred US pilots and carriers from flying in areas of Iraq, Iran and some Persian Gulf airspace, warning of the “potential for miscalculation” for civilian aircraft.
Several airlines from other countries have suspended flights over airspace in the region.
It is not known exactly how many EU nationals or EU staff are currently in Iran or Iraq, but the Commission spokesman said, “The EU is determined to continue its commitment in the region and is not going to pull out.”
“The EU is determined to continue its commitment in the region and is not going to pull out” European Commission spokesman
Tensions have been mounting in the Middle East after US forces killed Iran’s top General, Qasem Soleimani, on 3 January.
Iran launched more than a dozen missiles at Iraqi bases hosting US and coalition troops on Tuesday, declaring the strikes to be retaliation for the killing of Soleimani.
Al-Asad airbase in Iraq’s Anbar province was hit 17 times, including by two ballistic missiles that failed to detonate.
The Commission met early on Wednesday to discuss the situation stemming from the tensions in Iraq, Iran, the wider Middle East as well as Libya.
Commission President Ursula von der Leyen and High Representative/Vice-President Josep Borrell issued statements after the 8am meeting.
“The current crisis deeply affects not only the region but all of us. And the use of weapons must stop now to give space to dialogue” Ursula von der Leyen
Von der Leyen stated, “The current crisis deeply affects not only the region but all of us. And the use of weapons must stop now to give space to dialogue. We are called upon to do everything possible to rekindle talks. There cannot be enough of that.”
The European Union in its own way has a lot to offer. We have established and time-tested relations with many actors in the region and beyond to de-escalate the situation.”
Borrell said, “The developments in Iran and Iraq and the whole region are extremely worrying. The latest rocket attacks on air bases in Iraq used by the US and the coalition forces are yet another example of escalation and increased confrontation – it is in no one’s interest to turn up the spiral of violence even further.”
Further comment came from Council President Charles Michel, who noted, “The cycle of violence, provocations and retaliations which we have witnessed In Iraq over the past few weeks has to stop. Further escalation must be avoided at all cost.”
“Iraq remains a very fragile country. Too many weapons and too many militias are slowing the process towards a return to normal daily life for Iraq’s citizens.”
“The developments in Iran and Iraq and the whole region are extremely worrying. The latest rocket attacks on air bases in Iraq used by the US and the coalition forces are yet another example of escalation and increased confrontation” Josep Borrell
“The risk is a generalised flare up of violence in the whole region and the rise of obscure forces of terrorism that thrive at times of religious and nationalist tensions.”
NATO Secretary General Jens Stoltenberg, speaking on the Soleimani killing, said, “This is a US decision. It is a decision taken neither by the global coalition nor NATO. But all allies are concerned about Iran's destabilising activities in the region.”
A NATO spokesman said, “We have temporarily suspended our training on the ground, and we are taking all precautions necessary to protect our people. This includes the temporary repositioning of some personnel to different locations both inside and outside of Iraq.”
On Tuesday, the foreign ministers of Britain, France, Germany and Italy held emergency talks on Iran and Libya in Brussels.
Dominic Raab, the British foreign secretary, said: “We condemn this attack on Iraqi military bases hosting coalition - including British - forces.”
His German counterpart Heiko Maas said that despite current tensions, it was “important” to safeguard the Iran nuclear agreement.
On Friday, an extraordinary meeting of EU foreign ministers will take place in Brussels. It is seen as a chance to hear the views of all 28 Member States on the Iran situation.