"While the [new Melbourne community] case announced today is not unexpected as a contact of a case announced yesterday, New Zealand officials have assessed that the most cautious option is to pause the travel bubble with Victoria as there are still several unknowns with the outbreak."
Hipkins said the Government understood the disruption this would cause affected passengers.
"It was a close call but the correct one given the current unknowns. The decision follows the travel bubble framework."
Meanwhile, Victoria's Covid-19 outbreak has grown again, with another four new cases.
Victoria Health confirmed the infections on Tuesday afternoon, bringing the state's total number of community coronavirus cases to nine. All are linked to the City of Whittlesea outbreak, and are in addition to the one new case announced yesterday.
"Genomic sequencing has confirmed the strain of the virus detected in the four cases announced yesterday matches the strain of a case in Wollert earlier this month, who contracted the virus in hotel quarantine in South Australia," a Victoria Health statement said.
"Extensive contact tracing continues for the individuals who have tested positive to Covid-19 in Melbourne's north yesterday. All are isolating at home."
Hipkins said that anyone in New Zealand who had been at a location of interest in Melbourne at the specified time should contact Healthline on 0800 358 5453 as soon as possible for advice on isolating and testing.
Anyone who had visited Melbourne since May 11 should monitor for symptoms and seek advice from Healthline if any symptoms developed, Hipkins said.
Hipkins said a Section 70 notice had been issued under the Health Act with a number of requirements for any person who attended a location of interest.
New restrictions in Melbourne
Earlier on Tuesday, Victorian authorities put in place restrictions, which came into force last night, limiting the size of gatherings and requiring the use of face coverings indoors, following confirmation of a fifth locally acquired case of Covid-19.
Whole-genome sequencing identified that the cases reported yesterday are closely linked to a previous case identified in the community in Wollert on May 11 after leaving managed isolation in South Australia, Hipkins said.
An epidemiological link has yet to be determined between these cases and there is currently no known link between people in the current outbreak and any of the exposure sites from Wollert.
The cases include a man in his 30s, a man in his 70s, a woman in her 70s and a preschool-aged child. All have the Indian variant of the virus.
Speaking to reporters in Dunedin on Tuesday morning, Prime Minister Jacinda Ardern said New Zealand health officials were "in close contact" with their counterparts in Melbourne.
She said the Government was having a "discussion as a team" as to whether the new cases in Melbourne would impact on two-way travel.
On Monday night, NZ's Ministry of Health advised Kiwis who have recently travelled to Victoria to check a growing list of locations of interest.
This is not the first time there has been a hiccup with the transtasman bubble.
In early May, quarantine-free travel between New Zealand and New South Wales was suspended for two days after new community cases were discovered in Sydney.
When the NZ Government unveiled its transtasman bubble plans, it laid out a contingency whereby quarantine-free could be paused in the event of an outbreak.
