Chief executive Penny Simmonds said she became aware of the matter after a tip-off from a member of the public in late February.
The Invercargill-based tertiary provider, which also has campuses in Christchurch, Queenstown and Gore, launched an investigation in early March into financial irregularities, but it was still too early to say who was involved, or how much might have been taken, she said.
"Our investigations are not at a stage that we can quantify a figure."
The SIT council, the SIT audit and finance committee, Audit New Zealand and the police had been informed, she said, "and a thorough investigation is taking place".
It was unclear whether any taxpayer money was involved.
Detective Sergeant Dave Nelson, of Invercargill CIB, said police were assisting to "identify if any offences have been committed".
"This will take some time to work through."
He confirmed a former SIT employee "who is now deceased" was under investigation for financial irregularities involving the maintenance of buildings.
He declined to reveal the dead person's name.
Tertiary Education Commission tertiary network director David Nicholson confirmed a TEC staff member had recently visited the SIT but had not been informed of any investigations.
"However, since that visit, SIT has informed the TEC of its actions in investigating this matter."
A Serious Fraud Office spokesman said the office was aware of the case but was not investigating.