The Ilumina HiSeq 2500 allows scientists to sequence DNA in 24 hours, using its ''rapid mode'' function, as opposed to the about 10 days it took with the sequencer the university bought two years ago.
The growing field of gene sequencing allows scientists to examine the genetic instructions that exist in all humans, animals, plants and bacteria.
The new piece of equipment is based at the university and used by New Zealand Genomics Limited (NZGL), a collaboration between the Government, Otago, Massey and Auckland Universities, which provides sequencing services for New Zealand commercial and academic researchers.
Genomics facility manager Becky Laurie said the HiSeq 2500 and the HiSeq 2000 bought two years ago were the only examples of their kind in New Zealand.
The newer model had a ''rapid mode'', which collected less information but allowed for much quicker sequencing, Dr Laurie said.
This could come in handy when there were tight deadlines, which in future could include testing for medical purposes.
''So if you ... needed a diagnostic on a patient and you needed some sequencing information which might tell you whether that person had a disease - you want that information quickly,'' she said.
A recent example where time was of the essence was when the PSA virus, which was devastating kiwifruit crops, needed to be sequenced.
The new machine came in handy when scientists had tight deadlines to meet. Having two machines also meant they could continue sequencing when one broke down - which was not uncommon, given the complexity of the technology.
''There is a huge amount of high-powered electronics, lasers, cameras, everything going in there, so they are liable to break down,'' she said.
It could be quite ''scary'' running the machines, because up to $40,000 worth of chemicals were used at any one time, meaning mistakes were costly.
Sequencer operator Les McNoe said the cutting-edge technology in the machines made them comparable to Ferraris.
The astonishing pace at which genome sequencing technology had developed was shown by the fact that, using the new machine, it took 24 hours to do what took the thousands involved in the first mapping of the human genome 13 years, Mr McNoe said.