McChrystal visited the site about 100 miles (160 kilometers) north of Kabul as European leaders already nervous about the escalating war demanded answers. Some called the airstrike - requested by the Germans and carried out by U.S. jets - "a tragedy" and "a big mistake" that must be investigated.
The bombing also sent shock waves through Germany ahead of national elections Sept. 27. Opposition politicians called for a thorough investigation, even as the defense minister insisted all the dead were militants.
After touring the bomb site - where villagers' yellow fuel cans still littered the river bank - McChrystal paid a somber visit to the Kunduz hospital, where he stooped low to talk with a 10-year-old boy whose arms and legs were swathed in gauze.
"While I was going to get the fuel, on the way I heard a big bang, and after that I don't know what happened," said the boy, Mohammad Shafi.
McChrystal whispered "tashakor," - thank you in the Afghan language of Dari - to the boy and left the room.
"Anytime anybody is hurt it is something that gives pause to everybody, particularly when they're young people, still children. And so you take it very seriously," McChrystal said. "So I take this entire effort as something that is a responsibility of our command, and a responsibility of mine, to try to protect Afghans."
Civilian casualties have dogged the U.S. and NATO mission in Afghanistan since the 2001 invasion. When McChrystal took command in June, he immediately issued orders aimed at reducing such deaths, and asked his troops to concentrate on protecting and understanding Afghan villagers.
The new approach appeared to help, but Friday's bombing threatened a major setback to McChrystal's goals.
"From what I have seen today and going to the hospital, it's clear to me that there were some civilians that were harmed at the site," McChrystal told reporters. He did not say if any civilians were killed.
"I think it's a serious event that is going to be a test of whether we are willing to be transparent and whether we are willing to show that we are here to protect the Afghan people," McChrystal added. "And I think that it's very important to me that we follow through on that."
German officials have insisted everyone killed in the attack were militants. Other NATO officials, though, have conceded that civilians likely died as well.
"There is no reliable information on numbers, but there's a good sort of a gut sense that there had to have been civilians that made their way just based on the anecdotal conversations we've been hearing," said U.S. Rear Adm. Gregory J. Smith, McChrystal's top spokesman.
During his visit to the site, McChrystal asked Smith how many people could be seen on the riverbank through the video feed from U.S. F-15E fighter jets that carried out the attack.
"We could see from the downlink about 120 people?" McChrystal asked.
"It was ebbing and flowing," Smith said.
Afghan officials at first said as many as 90 people died in the bombing, though the Kunduz governor lowered his estimated toll on Saturday to about 70.
Smith said a preliminary review of surveillance video showed that 56 people died in the blast. But no U.S. or NATO official would say how many might have been civilians. McChrystal's reference to 120 people at the site suggests that officials believe civilians died because militants rarely congregate in such numbers.
NATO officials said a B-1 bomber first spotted the two stolen trucks and the dozens of people around them. The B-1 was low on fuel and had to return to base, but the two F-15Es arrived 20 minutes later. The jets transmitted video back to officials at the German base. About 30 minutes after the F-15s appeared, the bombs were dropped, at about 2 a.m.
The nighttime video would have been grainy. Smith described it as showing dark spots on the screen. "You can see shapes," he said.
McChrystal said it's hard to tell who is an insurgent solely by dress.
"They are not obvious by actions until they are doing the hostile act," McChrystal said. "This particular activity occurred about 2 o'clock in the morning, so you have the natural confusion of dark and a rural environment as well. So it's a challenge, but it's a challenge that we have to take very seriously and try to take as much care as we can."
Smith said the upcoming investigation would show if any language barriers between the Germans and the American pilots played a role. It hadn't yet been decided which NATO nation would lead the investigation, he said. Afghan officials were expected to take part.
Before traveling to the site of the bombing, McChrystal met local Afghan leaders and expressed sympathy for any civilian losses. He said the fight against the Taliban should not come at the expense of civilian lives.
At least one local official supported the allied bombing, saying it would help drive the insurgents from the area.
"If we did three more operations like we did yesterday morning, the Kunduz situation would be peaceful and stable," said Ahmadullah Wardak, a provincial council chief.
That was not a view shared by many European leaders, who called Saturday for a speedy investigation. French Foreign Minister Bernard Kouchner said the airstrike was "a big mistake." EU External Relations Commissioner Benita Ferrero-Waldner called the incident "a great, great tragedy."
German Defense Minister Franz Josef Jung insisted in comments to the Bild am Sonntag weekly that officials had no information indicating any civilians died in the airstrike.
Also Saturday, NATO said two U.S. service members were killed in separate attacks in Afghanistan.
Associated Press writer Frank Jordans contributed to this report from Kunduz.