South Korea is facing pressure to let the justice system take its course, instead of protecting a diplomat accused of sexual assault in New Zealand.

A spokesman for Prime Minister Jacinda Ardern told the Herald she raised the matter with Korean President Moon Jae-in in their phone conversation last week.

"She expressed her disappointment that the Korean Government was unable to waive immunity to allow aspects of the police investigation into this matter to proceed," the spokesman said.

"The matter now rests with the Korean Government to determine any next steps."

Hongkon Kim, the former Deputy Ambassador to New Zealand is accused of three counts of indecent assault at the Wellington embassy in 2017.

The charges relate to alleged incidents involving a male staff member at the embassy.

A warrant for his arrest was issued by a Wellington District Court judge in late February.

However, Kim had pleaded not guilty to the charges and remains overseas.

The Korean Government has so far refused to co-operate in getting him back to New Zealand to face trial, and he has instead been posted to the Philippines where he is currently serving as Consul-General.

The Ministry of Foreign Affairs and Trade said New Zealand "has made strong representation about this case" to the South Korean Embassy and the South Korean Government in Seoul, including both the Ambassador to Seoul and the South Korean Ambassador in NZ.