Jones blamed insurgents for the killing of civilians in southern Kandahar province, saying they had been using ordinary people as cover to avoid International Security Assistance Force fire.
Typically, "insurgents do not play by the same rules that we would like to play by," Jones told reporters at the end of a three-day trip to Afghanistan during which he met President Hamid Karzai and military leaders.
"In this particular case, sadly there appears to have been loss of life and innocent people who were wounded in a legitimate mission where insurgents were using the cover of the civilian population to make it very difficult for us to get at them."
Karzai has appointed a commission to investigate civilian casualties in the strike in the Panjwayi area late on Tuesday. The interior ministry has said about 25 were killed while the NATO force has said it knew of 12 deaths.
The International Security Assistance Force has said about 70 people were killed in a series of engagements that day, and it believed the vast majority were insurgents.
Jones, who had earlier received from Karzai Afghanistan's highest honour for his services to the country, said military commanders did what they could to avoid involving civilians in battle.
"Sometimes in the heat of battle, the fog of war, in the middle of the night when it is hard to separate one from the other, you make a decision on the spot," he said.
"That innocent people were wounded and killed is to be regretted and investigated. I personally apologise for the incident, for any loss of life."
The incident, about the fifth in nearly two weeks that has caused civilian casualties, comes as ISAF is trying to win "hearts and minds" to shore up the government and international community's efforts to keep the Taliban from regaining power.
"We will look into it and we will always do whatever we can to minimise any innocent people from being victimised in any way by military activities," Jones said.

Copyright AFP (Agence France-Presse), 2006