Sujiro Seam presented his letters of credence to the President of the Republic of Vanuatu, Moses Obed Tallis in Port-Vila.
He also met with Vanuatu's caretaker prime minister, Charlot Salwai.
According to Mr Seam, they had an in-depth discussion covering taxation, illegal fishing and passports.
The EU sought a closer relationship with Vanuatu beyond development co-operation, to gradual integration in the global economy and deepening political dialogue, he said.