At a meeting last week, the association executive also voted to withdraw from the NZUSA, a move which requires 12 months' notice before it can take effect.
The Otago student organisation, with about 22,000 members, is the biggest single contributor to overall NZUSA membership income.
It currently provides about $4.50 a head - about $90,000 a year- to the national organisation.
Associate membership requires much lower payments - about $2 per student - potentially cutting Otago funding support to about $40,000.
The earliest the NZUSA's federation executive can consider any Otago application for associate membership is at a meeting next month.
NZUSA co-president David Do said the OUSA executive move was "very disappointing" and not in line with indications Otago students gave in a recent Internet referendum about who should decide the relationship between OUSA and NZUSA.
The OUSA was one of the NZUSA's founding associations and had long been a much-valued contributor to the national body.
Applications for associate membership were not granted automatically - usually only in special circumstances, such as for the Auckland University Students Association, which had limited ability to pay because its campus had already adopted voluntary association membership.
Asked if the Otago move could harm the NZUSA financially, Mr Do said the need for all students to work together nationally to promote student interests was more important than the funding alone.
The Otago executive vote comes against a background of rising anxiety among student associations about the likely financial effects of proposed new legislation requiring voluntary membership of student associations.
A second reading of the Education (Freedom of Association) Amendment Bill, promoted by Act New Zealand MP Heather Roy, was almost completed last week and the Bill is close to becoming law.
OUSA president Harriet Geoghegan said the association did not wish to damage the NZUSA but the national body and its constituent associations had to adapt to rapidly changing circumstances, with the voluntary student membership (VSM) Bill about to become law.
OUSA executive members last week also voted for the OUSA to continue to work constructively with the NZUSA to address its issues and improve its service to the OUSA.
The OUSA would also investigate rejoining the NZUSA as a full member pending the outcome of an NZUSA internal review, providing that was completed by the NZUSA conference next January, the executive decided.
Ms Geoghegan said it would be "totally unfair" of the NZUSA to require the OUSA to provide funds which it could not guarantee to deliver when the VSM law fully came into effect in 2012.
The OUSA had had several concerns with NZUSA for some time, including the late completion of the NZUSA's latest annual audited accounts, she said.
Mr Do said the NZUSA was working to address any Otago concerns and the internal review would be completed by January.
The Otago executive's vote follows a recent Otago association online referendum during which 42% of participating Otago students voted to leave the NZUSA and 40% voted to remain.
It failed, by 48 votes, to reach the requisite quorum of 1049 votes, the magazine Critic reported.
Another motion - which missed a quorum by 31 votes - suggested "that matters of nationwide representation are best decided by the student body" and attracted 66% support, with 16% voting against and 16% abstaining.