The letter was a response to a protest from the Associated Press which had employed the two freelance journalists who were forced to delete photographs and video footage of the incident in Barikaw, eastern Afghanistan on 4th March.
Thirty-four people were also wounded in the violence.
Petrenko said that photographs or video taken by "untrained people" might "capture visual details that are not as they originally were".
Kathleen Carroll, the Associated Press executive editor in New York, disputed the assertions.
"That is not a reasonable justification for erasing images from our cameras," she said.
"AP's journalists in Afghanistan are trained, accredited professionals working at an appropriate distance from the bombing scene. In democratic societies, legitimate journalists are allowed to work without having their equipment seized and their images deleted."
Afghan witnesses and gunshot victims said US forces fired on civilians in cars and on foot along a 10km stretch of road from Barikaw after a suicide attack against the US Marine convoy.
The US military said its troops were fired at after the bombing. One Marine was wounded.Deleted footage
The footage that was deleted showed a civilian four-wheel drive vehicle in which three Afghans were shot to death about 100m from the blast.
Petrenko said that if people who are not part of the investigation entered such a "secured area" they could disturb evidence and other clues, "potentially fouling the conclusions of the investigation".
The journalists say they had complied with requests from the military to not move any closer to the bomb site.
Other Afghan journalists said soldiers also deleted their footage.
Petrenko maintained that the US military had no intention of curbing freedom of the press in Afghanistan.
"We are completely committed to a free and independent press, and we hope that we can help encourage this tradition in places where new and free governments are taking root," he said.Nato apology
Meanwhile, a spokesman for Nato forces in the southern province of Kandahar has apologised for the killing of civilians during military operations.
|"Isaf obviously apologises for what we've done there and we do get in touch with the families"|
Community leaders in Kandahar told Al Jazeera that at least two innocent Afghans die every week when Nato forces mistake them for suicide bombers or Taliban fighters.
The apology came six days after an airstrike north of Kabul killed nine members of the same family.
"Isaf obviously apologises for what we've done there and we do get in touch with the families, there are chats with the families and individual nations who've been involved in the action," Wing Commander David Marsh, Nato-Isaf spokesman, told Al Jazeera.
"We're doing everything we can, I believe, to try to stop this kind of activity from continuing," he added.