"The only issues that we can confirm at this stage - there was no hostile action, no operational incident that caused his death.''
At least one other person had been with Corporal Hughes when the incident occurred, but General Jones would not reveal what they had said about the incident.
No one else was believed to be involved in his death.
"At this stage we are still gaining that information, still going through that inquiry. There is a process for us to go through to be able to confirm exactly what happened, and to make statements before that can be confirmed officially is premature.''
General Jones would not say what injuries Corporal Hughes suffered or whether a firearm was involved.
Those types of issues needed to be confirmed by the coroner, and Corporal Hughes' family would be informed first.
General Jones said Corporal Hughes did not have a history of mental health issues, and he was not believed to be on watch at the time, although that was unconfirmed.
"At this stage we don't think that it was an operational pressure issue.''
It was not known how long the investigation would take.
Corporal Hughes, a rifleman from the 1st Battalion Royal New Zealand Infantry Regiment based at Linton Military Camp, had been in the army for nearly eight years.
General Jones said he had previously been deployed in the Solomon Islands and once before with the Provincial Reconstruction Team in Afghanistan.
He was deployed to Afghanistan for a second time last September and was due back to New Zealand later this month with the rest of his contingent following a six-month deployment.
The Defence Force had notified the immediate families of all soldiers involved and was providing assistance to them.
Corporal Hughes' body remained at Bagram air base while arrangements were made for his repatriation.
General Jones extended his sympathies to Corporal Hughes' family, colleagues and friends.
Corporal Hughes, known as Dougie, was unmarried with no children and was survived by his parents, a brother and sisters.
His family in Northland released a statement.
"We are very saddened by the loss of our son Dougie. He was a talented sportsman with a good sense of humour who lived for his career in the army.''
Defence Minister Jonathan Coleman said it was a tragic day for the Defence Force and Corporal Hughes' family.
"He was young man with a very bright future ahead of him and this is an absolute tragedy,'' he said.
Dr Coleman extended his condolences to the family on behalf of the Government, saying the death had come as "a major shock''.
"Corporal Hughes' death is going to be taken extremely hard by the PRT in Afghanistan, and also at Linton, which was his home base.''
Prime Minister John Key described the death as "a very tragic circumstance''.
"I can't really say too much more about that for obvious reasons.''
"Beyond that, we would want to make sure that if he was experiencing difficulties he was getting the appropriate level of pastoral care from his superiors on the ground. My experience of being up there is they're very well led in the PRT but we'll just want to follow up on that obviously.''
RSAs throughout the country flags will fly at half-mast over the next few days.
RSA national president Don McIver said the news of Corporal Hughes' death would be received with great sorrow by all its members.
"Our deepest sympathies are with all those who loved and cared for Corporal Hughes - his family, friends and comrades," he said.
- Additional reporting New Zealand Herald
