The scientists achieved their aims by drilling two adjacent boreholes to depths of 101m and 152m on river terraces next to Gaunt Creek, near Whataroa, in late January and early last month.
They collected rock cores during the drilling.
They also installed permanent monitoring instruments to record temperatures, pressures, and seismic activity inside the boreholes before back-filling both holes.
Co-leader of the Deep Fault Drilling Project, Dr Rupert Sutherland, of GNS Science, said the project was "an overwhelming success".
"We were astonished that we managed to collect such high-quality rock cores across a zone that has been smashed by literally thousands of magnitude 8 earthquake movements over millions of years," he said.
Dr Sutherland, who is an Otago geology graduate, said drilling through the Alpine Fault had never been done before and the work had required improvising "in good old Kiwi fashion", but had finished on schedule.
Analysis of the data obtained would enable scientists to make better calculations of what actually happened during future large earthquakes.
The scientific analysis would eventually "turn into engineering standards and other preparations that mean New Zealand will be better prepared for the big quake when it happens," he said.
Assoc Prof John Townend, of Victoria University of Wellington, is an Otago geology graduate and is also a project co-leader.
Prof David Prior, an Otago University geologist involved in the project, said the recent destructive earthquake and tsunami in Japan highlighted the need to continue this kind of basic research into the origins of earthquakes, and the way different types of rock contributed to significantly different outcomes.
Dr Virginia Toy, another Otago geologist, and a project co-leader as well, said the success of the project's $300,000 first phase gave a green light to the planned $2 million second phase, involving much deeper drilling into the Alpine Fault, which is due to start next year.
The recently-collected rock cores, weighing about 3.2 tonnes, have been transported to Otago University where they are being analysed by a $300,000 core-scanning machine.
The collection of 360deg images of the core surface and scans of the rocks' physical properties are being co-ordinated by Dr Toy.
