Its chief executive Rob Facer said he had not directly been in touch with the student's family.
"We have a representative in New Zealand who has been liaising with the family in Malaysia," he said.
"My understanding is that two of his immediate family members are coming out to New Zealand to transport his body back to Malaysia."
The company had commissioned "a thorough" internal investigation, Mr Facer said.
They were also assisting regulatory authorities to ensure the relevant information was made available to them "as and when they need it".
The student, who was a qualified recreational diver, had undergone a "very thorough and comprehensive medical" to do the commercial diver course.
He passed the medical test, but Mr Facer would not say whether the student had any medical issues.
A company spokeswoman said conditions at the lake yesterday were calm.
All students had to have passed recreational diving courses before starting the commercial courses, she said.
Until the dead student had been formally named, she would not give any details on which course he was doing.
The company had "stringent regulations" in place while courses were being undertaken, she said.
"Out of respect for the family and what has occurred, we have no formal classes for the rest of this week, and on Monday classes will resume."
No students had pulled out of the course since the incident, she said.
A WorkSafe NZ spokesman said they were notified of the incident yesterday and they had sent out an investigator.
No further details were available as the investigation was pending, he said.
Lake Puketirini is a newly formed lake that had been developed from a disused coal-mined pit, and was now part of Puketirini, a Waikato District Council owned park, the council website said.
The lake was available for activities such as kayaking, waka ama, boating, and water-skiing.
