Mr Scott, who is a former long-serving member of the University Council, was commenting in a hard-hitting address at a university graduation ceremony on Saturday.
Accountants and merchant bankers in New Zealand had "little time or patience for scientists" and that feeling seemed "very much mutual", he had found.
"This must change," he urged.
He was at present involved in fundraising for a New Zealand-registered biotech company whose science had come from Auckland University.
New Zealand banks and financial institutions had shown no interest in providing funding.
The company had been forced to list on the Australian stock exchange, with its main funding coming from Australian and United States investors.
"The banks and financial institutions in New Zealand that showed no interest were in most cases run by commerce graduates from New Zealand universities."
Innovation was a central driver for New Zealand's productivity and growth, and science was "not just an indulgence but is the core of our economic development".
"Collaboration between science and commerce, therefore, is essential," he said.
Mr Scott said universities were involved in the discovery and dissemination of knowledge, and some of this knowledge was commercially valuable.
Otago University's consulting and commercial revenue at present amounted to about $12 million a year, an important contribution to the university's income in times of funding constraints.
He recalled that after working as a chartered accountant he had initially had little contact with the university since graduating from Otago with a bachelor of commerce degree in accounting in 1964.
He had then, in 1986, been asked to review the university's commercial activities and found that most of that at the time was "buried deep in the departments and jealously guarded".
The review resulted in the establishment of the university's Commercial Activities Board, and, later, the forming of Otago Innovation Ltd, both of which he had subsequently chaired.
Prof Sir Peter Gluckman, the chief science adviser to the Prime Minister, had recently commented that there was a lack of genuine expertise in New Zealand in technology transfer.
Mr Scott said that despite increased efforts over the past decade, New Zealand had a relatively poorly performing innovation and science infrastructure and was not yet making as much of an effort as other small countries.
In the past, new technology had mainly displaced manual workers, and the human mind was the most important resource in many of the remaining occupations.
He urged science and commerce graduates to stay ahead by working together.
Mr Scott received an honorary doctorate of laws, and more than 470 graduands, mainly in sciences, commerce and consumer and applied sciences, graduated in person atthe ceremony in the Dunedin Town Hall.
