Brig Gen Carsten Jacobson, spokesman for the NATO-led International Security Assistance Force, said an investigation had been launched.
The main issue at the NATO conference, and one that the president stressed, is Afghanistan.
Mr Flynn made his remarks during an urgent question on the Nato strategy in Afghanistan.
Many of the NATO-led countries provided enough troops specifically to provide security for the election season.
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It was much the same earlier in the week at the NATO summit in Brussels.
But the Nato Response Force will also act as an important catalyst for change.
France, along with Britain, took a leading role in the NATO-led air campaign against Gadhafi's forces.
Is the western press being unfair in its portrayal of the Nato effort in Afghanistan?
If the SNP cannot accept the Nato Strategic Concept then it will simply not get in.
Gen Petraeus was stationed there before he moved to Afghanistan to run the Nato operation.
The NATO Secretary-General spelled out exactly what Bosnian Serbs must do to avoid further air strikes.
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Ukrainian President Viktor Yushchenko said his country should be able to start the NATO membership process.
The official spoke on condition of anonymity because the NATO investigation was not complete.
Few, if any, Western allies would consider contributing troops outside the NATO framework, diplomats say.
As per Lisbon and the NATO agreement, that will be by the end of 2014.
The NATO alliance has grown at the summit to include two new members, Albania and Croatia.
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He was in Dresden, he was in Buchenwald, he was in Baden-Baden for the NATO conference.
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Some German troops from the NATO defence alliance's peacekeeping force in Afghanistan were also being sent.
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One reason is Mr Sarkozy's decision to return France fully to the NATO fold.
Meanwhile, Pakistan remains angry over the Nato attack which on Wednesday it described as "deliberate aggression".
Russia is not a NATO member but works with the alliance via the NATO-Russia Council.
They fled the NATO bombing campaign and the depradations of the Kosovo Liberation Army.
And he killed the NATO-agreed missile defense plan for defending Europe and the United States.
So there are a variety of ways that we continue to assist the NATO mission.
In part it is simply that he wants Europe to pull its weight in the Nato alliance.
Another coalition service member was killed in an insurgent attack in northern Afghanistan, the NATO-led force said.
But the Nato commander in Helmand Major-General Richard Mills, was bullish in his analysis of the war.
Outside the NATO meeting, protesters marched and rallied on Monday, a day after violent clashes with police.
However, Obama and Zardari had a brief conversation Monday morning on the sidelines of the NATO session.
Correspondents say this is the first such incident since the Nato-led peacekeepers entered the province last June.
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