The military said some personnel involved "failed to comply with the rules of engagement and the law of armed conflict," and that a general officer was among those facing discipline for their roles in the bombing of the Doctors Without Borders hospital.
The punishments include suspension and removal from command, letters of reprimand, formal counseling and extensive retraining. These punishments would have adverse effects on promotion of the personnel involved, according to the U.S. military.
Twelve of the punishments were administered by U.S. Forces Afghanistan, while the remainder were carried out by U.S. Special Operations Command.
Gen. Joseph Votel, commander of U.S. Central Command, made the announcement at a news conference in Washington. The investigation had identified 16 service personnel that had "warranted consideration for appropriate administrative or disciplinary action."
"The comprehensive investigation concluded that this tragic incident was caused by a combination of human errors, compounded by process and equipment failures," Votel said in explaining the decision not to regard the incident as a war crime. He also said that the aircrew were "unaware" that they were firing on a hospital.
The hospital was operated by the non-governmental organization Doctors without Borders, also known as Médecins Sans Frontières (MSF), which was located approximately 400 meters from the intended target, a Taliban-controlled site, according to the report.
Doctors Without Borders says that more than 100 patients were admitted to the hospital when it was struck.
Pablo Marco, operations manager for Doctors Without Borders in the Middle East, told CNN Thursday that his group would continue to push for an independent external investigation into the strike.
"We just need to remember that since the beginning, MSF has asked for an independent investigation to really understand and to make clear what happened in Kunduz and that unfortunately despite the fact that the U.S. has had an internal investigation, this independent investigation hasn't happened yet and we keep asking for it," he said.
At the news conference, Votel stressed, "We extend our deepest condolences to those injured and to the families of those killed in this tragic incident," adding that the Pentagon was "fully committed to learning from this tragedy and minimizing the risk of civilian casualties during future combat operations."
"This was an extreme situation we were dealing with," Votel said, noting that the Taliban in the area were in possession of a surface-to-air missile, a rarity in the Afghanistan conflict.
He noted that the investigation was overseen by then-commander of U.S. forces in Afghanistan, Gen. John Campbell, and was carried out by three U.S. generals who "were brought in from outside Afghanistan in order to provide an objective perspective." The investigators interviewed 65 witnesses, including personnel at the trauma center and members of U.S. and Afghan militaries, and reviewed thousands of documents.
According the report, "The investigation found that the tragic incident resulted from a combination of unintentional human errors and equipment failures, and that none of the personnel knew that they were striking a medical facility."
The Pentagon concluded last year that Doctors Without Borders had followed all proper procedures in notifying the U.S. of the location of the hospital. The group "did everything right," a U.S. official said in October.
Votel said that Campbell had directed a review of the targeting process, rules of engagement, condolence payments to more than 170 individuals and families affected, and $5.7 million to be allocated for the construction of new medical facilities in Kunduz.
Votel added that "senior U.S. representatives have spoken with MSF officials, including the MSF Executive Director, over two dozen times to express condolences, explain how the tragic incident occurred, and outline future steps."
Campbell's successor, Gen. John Nicholson, met with families of the victims from the attack and issued a personal apology
shortly after assuming command in March.
"I grieve with you for your loss and suffering; and humbly and respectfully ask for your forgiveness. We mourn the death of any Afghan, but the death and wounding of innocent Afghans because of our mistake is extremely painful to us," he said at the time.
"As commander, I wanted to come to Kunduz personally and stand before the families, and the people of Kunduz, to deeply apologize for the events which destroyed the hospital and caused the deaths of the hospital staff, the patients and their family members."
Secretary of Defense Ash Carter said in a statement, "I want to once again express my deep condolences and regret for the loss of innocent life."
"The U.S. military takes the greatest care in our operations to prevent the loss of innocent life. When we make mistakes we must own up to them and hold individuals accountable as necessary," he added, nothing that he had directed "a number of specific actions to ... mitigate the potential for similar incidents in the future."
"This report provides important and painful lessons, and as I have directed senior leaders across the Department, we will now act upon them," he said.
MSF issued its own statement after the press conference, saying it "acknowledges the U.S. military's efforts to conduct an investigation into the incident," but added that the organization "has said consistently that it cannot be satisfied solely with a military investigation into the Kunduz attack. MSF's request for an independent and impartial investigation by the International Humanitarian Fact Finding Commission has so far gone unanswered."
"U.S. forces failed to follow the basic rules of war," MSF president, Meinie Nicolai, said in the release, adding that "armed groups cannot escape their responsibilities on the battlefield simply by ruling out the intent to attack a protected structure such as a hospital."
The statement slammed the level of discipline administered to U.S. forces involved, calling it "out of proportion to the destruction."
"The administrative punishments announced by the U.S. today are out of proportion to the destruction of a protected medical facility, the deaths of 42 people, the wounding of dozens of others, and the total loss of vital medical services to hundreds of thousands of people. The lack of meaningful accountability sends a worrying signal to warring parties, and is unlikely to act as a deterrent against future violations of the rules of war," the statement said.
It concluded by saying that "it has become clear that the victims and their families have neither the option to pursue legal action against the U.S. military, either in Afghanistan or in the U.S., nor to claim compensation for loss of life and livelihood. This has only compounded the devastation of the attack."
The investigation report comes as another Doctors Without Borders hospital in Syria was bombed this week, a strike that the NGO says killed 50 people and was carried out by Russian and Syrian warplanes. "This hospital is very well known," Marco said, adding that there were "many chances that this was deliberate."
Correction: An earlier version of this story incorrectly stated the number of U.S. service members to be disciplined.