The MED blamed the outage on upgrade work to the servers hosting the sites.
While the MED is apologising "unreservedly", intellectual property consultant Murray Stott said someone needed to be held accountable for the fault.
Stott claimed he used the websites for up to 4 hours each day and said the outage was unacceptable.
"Internationally, it's not a good look," he said. "They're pushing towards having everything put online, if it fails they should have a manual system or a backup system in place. This is completely unsatisfactory."
The Intellectual Property Office website was also down earlier in the year, but for nowhere near as long as this outage, Stott said.
Baldwins Intellectual Property partner Penny Catley said the firm had backlogged work that could not be completed because of the fault.
The company had to explain to clients in New Zealand and overseas that some work would be held up.
BusinessNZ chief executive Phil O'Reilly said the outage, particularly of the Companies Office website, was concerning. "Companies regularly rank [the Companies Office] as the most business-friendly part of the Government bureaucracy. The problem with that is people rely on its services. It's concerning there wasn't a backup plan for this type of outage and I certainly hope they move on and get it fixed as quickly as then," he said.
While a four-day outage would be more of an annoyance than a disaster for businesses, O'Reilly said companies would want to know the problem will not happen again.
"It will be important that the Companies Office not only get up and running as quickly as possible but that they can then reassure businesses that they've got a plan to make sure it doesn't happen again," he said.
Commerce Minister Simon Power said an investigation into the cause of the fault would take place.
"I've been advised that MED is doing everything it can to get the websites back online as soon as possible, and that they will be investigating what caused the outage to avoid a recurrence," he said.
SYSTEMS DOWN
Government websites down from Saturday night until at least midday today:
* Companies Office
* Personal Property Securities Register
* New Zealand Petroleum and Minerals
* Intellectual Property Office of New Zealand
* Financial Service Providers Register
* Insolvency and Trustee Service
* Radio Spectrum Management
* G2B
* The Ministry of Consumer Affairs
* Business.govt.nz
* Government Procurement Solutions
* Motor Vehicle Traders Register
* Societies and Trusts
* Volunteer Net
* Business Data
