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.
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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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.
Russia is not a NATO member but works with the alliance via the NATO-Russia Council.
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.
The NATO peacekeepers had been marking the border with Serbia when they came under fire on Friday.
The NATO members also agreed to devote a fifth of their defense spending to major equipment purchases.
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"The Americans are concerned about the core strategy being approved by everyone involved, " said the Nato official.
Russia is not a member of NATO but is a member of the NATO-Russia Council, formed in 2002.
The Nato-led International Security Assistance Force (Isaf), which oversees operations in Afghanistan, said the commander's email was "prudent".
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The NATO meeting assessing the Serbs' compliance with NATO's demands is over, but there is still no action.
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