Scientists will today begin an ambitious project to drill boreholes into the South Island's Alpine Fault, hoping to find out more about how an active fault reacts before and during an earthquake.

The group of international and New Zealand scientists will drill directly into the massive faultline to investigate its structure, mechanics and evolution.

"We don't know what we'll find when we drill into the Alpine Fault. If we knew all the answers, we probably wouldn't be doing this," said project leader Rupert Sutherland of GNS Science.

The boreholes will be about 130m to 180m deep and up to 60m apart at Gaunt Creek near Whataroa, north of Franz Josef on the West Coast. It was the first time scientists had investigated a major active fault in New Zealand by drilling boreholes, he said.

The team planned to install sensors within one of the boreholes to create an underground "observatory" by mid-February.

"This summer is the first step in an exciting long-term project where a New Zealand-led international consortium will drill to progressively greater depths into the Alpine Fault to better understand how large faults work," he said.

Next summer, the group planned to drill about 1.5km into the fault.

Scientists hoped the project would help them understand more about the physical and chemical processes that took place at a fault before and during an earthquake.

"There is considerable international interest in our project at Gaunt Creek as it has the potential to answer a number of important questions about plate boundary earthquakes and the evolution of large faults."

Scientists have previously talked about the potential to drill a borehole up to 5km deep, which could give new clues about what happens in the lead-up to a major quake 10 times as powerful as Canterbury's 7.1-magnitude quake on September 4 last year.

The Alpine Fault, running the length of the South Island, has not produced a large earthquake in three centuries but is regarded as one of New Zealand's most hazardous faults.

The Government has been told that there is a 20 per cent chance of a big quake on the fault in the next 20 years, compared with a 15 per cent chance of a major one affecting Wellington over the next 50 years.

The Alpine Fault runs for more than 650km, from south of Fiordland and along the spine of the South Island into Marlborough. It has moved an average of 27mm a year over the past 50,000 years - but this has included catastrophic quakes in which it has moved 8m in seconds.

It ruptures every 200 to 400 years - producing earthquakes of about magnitude 8 - most recently in 1717 along nearly 400km at the fault's southern end.

A similar project at Parkfield on California's San Andreas Fault cost $44 million and has equipment inserted 3km deep.