A spokeswoman for Customs said the JBMS was supposed to be delivered to Customs and MPI in November 2012 but "change and delays are to be expected with a programme of this size''.
The decision was made in June 2012 to split the release date into multiple stages because of the "risks of delivering such a complex system with many interdependencies'' and the first stage was scheduled for April 2013.
The first stage of the Trade Single Window, described as a 'one-stop-shop' for importers and exporters to directly enter information through an electronic screen, was pushed back to June 17 and again to August 1.
Cabinet papers released under the Official Information Act show this cost taxpayers around $1 million a month in lost revenue and the June delay led to a crisis meeting between Customs, MPI and IBM.
"The reason for the delay is the latest testing phase has not run to schedule and officials wish to ensure the implementation is fully tested and a robust solution is in place. The criteria established for a satisfactory release have not been met,'' according to the documents.
There was not one single cause for the "changes to the timeframe'', the spokeswoman said told the Weekend Herald, but the integration with existing systems were more complicated than expected, so have taken longer to develop and test.
She said more work was needed to strengthen security, New Zealand was the first to adopt new international trade data was challenging and requested changes to the system also needed more time.
However, the risk and intelligence "core'' of stage one of the JBMS has still not been delivered.
Concerns about this aspect of the "largest information technology programme ever undertaken by Customs'' were first flagged in April 2012 by a review conducted on behalf of the State Services Commission.
The Performance Improvement Report said the JBMS was well advanced to meet the 'go live' date of April 2013, but noted the Trade Single Window was the less risky component to deliver on time.
But the author said it was "concerning to hear that the scope of the risk and intelligence tools'' had not been finalised.
"Adding to this, we were advised that the main contractor was having difficulty in bedding down these new tools and although we were not able to explore this in any detail, it is an issue which Customs needs to address,'' said the report.
"There are many examples of information technology programmes having struggled or failed due to poor scope control and scope control for JBMS should be addressed as quickly as possible. The scope should be locked down and any further changes should only be agreed at the most senior level and only for absolutely essential changes.''
The spokeswoman said Customs was committed to delivering the full set of JBMS risk and intelligence technology to monitor the border.
She also pointed out other advanced risk assessment tools established in recent years, including the Integrated Targeting and Operations Centre (ITOC) which is a multi-agency group.
However, another State Services Commission review noted the ITOC was in a "relatively early stage of development with respect to improving the use of intelligence'' and many systems would remain "administrative in nature'' until the JBMS was operating.
The delays in establishing the risk and intelligence tools come as hundreds of kilograms of drugs were smuggled into New Zealand by shipping container.
Operation Ghost discovered 330kg of pseudoephedrine, a Class-B drug used to cook methamphetamine, hidden in three safe houses across Auckland. Detectives believe another 142kg shipment was imported in May and, along with Customs' staff, stopped another 248kg consignment at the Ports of Auckland on Sunday.
Customs Minister Maurice Williamson issued a press statement about the second drugs haul which mentioned the "intelligence tools and methods being used by Government agencies have improved out of sight in recent years''.
However, the Weekend Herald understands the intelligence gathered to identify the most recent shipment was mainly from intercepted phone calls, covert surveillance and physical evidence discovered when properties were raided.
The discovery of such large caches of pseudoephedrine are at odds with previous statements from the Minister.
In a press statement in October 2012, Mr Williamson said Customs had stopped 300kg of pseudoephedrine in that year so far - down from a record of 1.2 tonnes in 2009.
"We believe measures the Government has taken since 2009 have resulted in the supply of precursors being constrained and it is reflected in the statistics''.
However, a 'Tackling Methamphetamine' report released by the Prime Minister in October said "the ongoing decline in the quantity of precursors seized is likely to be a reflection of a change in modus operandi by the syndicates involved, rather than an indication of reduced quantities entering New Zealand.''
A spokesman for Mr Williamson said he stood by his previous statement.
"There's clear evidence that the methamphetamine market is now smaller than it once was and the efforts of the Government are having an impact.''
Evidence previously cited is a drop in methamphetamine users from 2.2 per cent of the population in 2007/08 to 0.9 per cent in 2012.
