A briefing provided to Clark on the cancellation of February's publication said that since October 2014, 66 million records had been processed but "data completeness and quality varies across DHBs due to DHB system variation and their ability to invest in data quality".
The system failed completely for two weeks in November, resulting in a backlog of files to be input.
"NPF application performance remains poor and not all DHB data submissions have been able to be loaded without significant intervention and rework," the briefing said.
The NPF is expected to improve patient flow through secondary and tertiary services by producing better data on demand, reasons for delays in patient access and gaps in care.
DHBs have been warned by the Health Ministry that not implementing the NPF will result in "significant financial and reputational consequences".
At this stage the data is being referred to as "developmental" and the data published in August comes with advice not to compare numbers between DHBs because of "gaps and inconsistencies".
Questions collated from monthly teleconferences with regional staff working on the NPF, as recently as July this year, show that the four-year-old system is still not bedded in.
Questions include:
• Are DHBs expected to retrospectively correct all data since the beginning of the project?
• Our DHB is still using remediation codes in some instances. Is this still acceptable?
• I'm not confident NPF is still considered a priority in my DHB. What communication does the ministry have planned with my DHB's Executive?
A spokesman for the ministry said: "The investment in the programme, over the four years of its development from July 2013, has been an average of $4.1m a year. Approximately half of that funding has been provided to DHBs and the remainder within the Ministry of Health to develop the IT systems and infrastructure to support the programme."
The NPF will eventually replace the National Booking Reporting System, which has been used since 2000 and is used mostly to monitor waiting times for elective services.
Canterbury Charity Hospital Trust chairman Phil Bagshaw, a surgeon, said there should be two pieces of data - what DHBs have done, and a regular national population survey on what isn't done.
"Then you can set your standards for what is expected of DHBs. It's very simple actually."
Bagshaw said no one paid any attention to the NPF anyway. "It's not really in the interests of the ministry to for it to be collected is it? Then people would realise how much isn't being done."
Clark said in a statement that the Ministry of Health continued to collect a large amount of data, and accountability measures were built into the health system.
"New health measures are in development. It is important to take time to get these right so that we avoid the perverse outcomes that can be created by a narrow set of targets.
Clark announced earlier this year that the Government was ditching the previous National government's national health targets, saying they were too narrow and could lead to "perverse outcomes" for patients.