NZSOS originally faced three charges, while Te Ripo faced four - two of which had a maximum sentence of two years' imprisonment or $500,000 fine.
However, the maximum sentence for both parties on their charges is now a maximum fine of $250,000.
Judge Burnett convicted NZSOS however, Fletcher Pilditch - counsel for Te Ripo - asked the judge to hold off convicting his client so that they could discuss filing for a discharge without conviction.
Te Ripo was contracted by the school as its dive supervisor on the day of the incident, while McKenzie and Weston were dive instructors.
Charges were first laid against the parties in October last year and it has resulted in multiple adjourned court appearances until yesterday.
It remains unclear why NZSCDT, Weston and McKenzie had their charges withdrawn.
NZSOS is a private training establishment [PTE] trading as the New Zealand School of Commercial Diver Training (NZSCDT) and is owned by Intueri Education Group Ltd, New Zealand's largest private training institution.
Intueri's chief executive Rob Facer told the Herald he was aware of the court delays but said he had been in contact with the victim's family and even travelled to Malaysia to see them.
"I've made a number of representations to the family in the period since the incident ... and I have actually been to Malaysia. We have provided an amount of support to the family but there are more things that we can do and work through."
Mr Facer said the conviction on NZSOS - which holds the diving accreditation from the Australian Diver Accreditation Scheme [ADAS] - would not affect its operations which had been reviewed since the incident.
"Our school operates to a number of accreditations, the principal one being ADAS and obviously there have been a number of reviews of the processes and policies and procedures for all the ADAS schools around the globe as a result of this incident ... and we have obviously adopted those updated standard operating procedures at the dive school since."
It was the first fatal incident at the dive school which had been operating for 15 years.
"And we hope that it will be the only ever incident of that magnitude. We must remember however that any occupation in a non-respiratory environment comes with inherent risk, so commercial diving is an inherently dangerous occupation hence the reason that we have all the protocols and safety procedures that we do and unfortunately there have been other tragedies at other dive schools around the globe over the years."