Starting in July, data collection would give the ministry a clearer picture of colonoscopy waiting times and volumes, Dr Childs said.
Dr Childs, who declined to be interviewed, said in a written statement the ministry would gather information pertaining to urgent, non-urgent, and surveillance colonoscopy.
"The Ministry of Health has begun a programme of work to ensure we can consistently collect information from DHBs, which will build a better picture of current capacity in the sector.
"The focus of this work is on improving how we monitor and measure wait times, and should not be seen as a report card for DHB performance."
Health Minister Tony Ryall, in a statement, said there was no national data on waiting times for the procedure at present.
"[The data collection] may result in a national target for colonoscopy wait times at some point in the future, but there are no plans for that now."
In 2009, Dunedin Hospital came under scrutiny over access to colonoscopy. A group of GPs had complained of patients at risk, sparking an independent audit.
Dunedin gastroenterologist Emeritus Prof Gil Barbezat, chairman of the Dunedin gastrointestinal diseases centre establishment board, said the situation had improved in the South, but national data collection would give patients and clinicians a better idea of how access varied throughout the country.
"There are clearly some [DHBs] who are up with the play, and others who are behind, and Otago Southland has been behind in the stakes in the past."
He agreed it was inevitable such data would be viewed as a "report card", but cautioned that DHBs counted procedures in different ways, so comparisons could be deceptive.
He also had "a little bit of sympathy" with DHBs, because of a lack of facilities and trained staff in some places.
"It is rather difficult if it is held as a report card, and you don't have the funding to do it."
Prof Barbezat said it would be a "mistake" not to also collect data pertaining to the less invasive diagnostic tool CT colonography.
"They should include [CT colonography]. They are less expensive than colonoscopy, but a number of patients will end up needing both."
It is hoped the Dunedin gastrointestinal centre of excellence, which is under development, would provide an additional endoscopy room in Dunedin, which would increase colonoscopy volumes.
Colonoscopy helps prevent bowel cancer deaths, because they identify and allow removal of polyps.
