Commerce and Consumer Affairs Minister Jacqui Dean said the GI legislation - due to come into force in late July - would show that a wine or spirit came from a specific region, "and possesses particular qualities or characteristics as a result''.
"Registering regional names for our wine and spirits will reinforce the qualities and reputation of these products, allowing winemakers to safeguard what is special and precious about their area ... It will also make it easier for exporters to promote and protect their wine and spirits in some overseas markets.''
Ms Coughlan said the COWA's application would be for "the entire Central Otago wine region, which encompasses the boundaries of both Queenstown Lakes and Central Otago District Councils''.
A spokesman for Mrs Dean's office said once applications were lodged they would take about six to nine months to process.
Much of this time would be spent defining the exact geographic boundaries of proposed GI areas, the spokesman said.
As well as applications for regions, individual or groups of wineries could also apply for GI recognition for smaller areas, such as Wanaka or the Gibbston Valley, the spokesman said.