The United Nations Committee Against Torture is asking the New Zealand Government to fully investigate the 2010 Afghan raid, as part of a list of issues to be responded to by 2019.
Hit & Run, by investigative journalists Nicky Hager and Jon Stephenson, alleges six civilians were killed and 15 were injured in Operation Burnham.
Further, it alleges that, supported by US and Afghan forces, the Special Air Service (SAS) burned and blew up about a dozen houses and failed to help the wounded.
The United Nations Committee Against Torture has released a list of questions for New Zealand to answer prior to an examination by the committee in Geneva. The date for the examination is likely to be in 2019.
The question relating to the Afghan raid allegations says:
"Please indicate what measures the State party has put in place to ensure that all allegations relating to 'Operation Burnham', a raid of two villages in the Baghlan province in Afghanistan by the New Zealand Defence Forces on 22 August 2010, will be fully investigated and addressed."
Foreign Minister Gerry Brownlee said in a statement that "the New Zealand Government has not been ordered to investigate the allegations made in the book Hit & Run".
Mr Brownlee said that the request was part of a list of issues that are a routine reporting process, and said that the request about Afghanistan was based on "factual inaccuracies".
He said the allegations made by Mr Hager and Mr Stephenson in Hit & Run have been disproven.
"The allegations made by Nicky Hager and Jon Stephenson were disproven and the Chief of Defence Force held a press conference detailing the New Zealand Defence Force raid in Afghanistan in 2010.
"I would also like to point out that the findings of the International Security Assistance Force investigation undertaken in 2010 after Operation Burnham were available to the United Nations Assistance Mission - Afghanistan at the time."
In April, Prime Minister Bill English said a classified video, which he will not release, confirmed that the New Zealand Defence Force personnel took all necessary precautions to ensure minimal opportunity for civilian casualties and destruction of property.
Executive director of Amnesty International New Zealand, Grant Bayldon, says the organisation disagrees with the claim there's no basis for ordering an inquiry into alleged war crimes.
Mr Bayldon says this development proves the matter isn't over yet.
"Amnesty International flatly disagreed, as did thousands of New Zealanders. Now the UN is calling on the Government to show how these allegations are being properly addressed. It's clearly the right thing to do. The families of the Afghan victims and the New Zealand public deserve nothing less."
He says it's not too late for Mr English to order a "thorough, independent inquiry".
"We have very real concerns about the impartiality of military forces investigating military conduct... We owe it to New Zealand's international reputation and the men and women who represent us in conflicts overseas to remove any shadow of a doubt about our military conduct."