According to Antara news agency, Retno Marsudi said Indonesia also had the right to explain.
This comes after last month's fiery response by Indonesia to speeches by some Pacific governments at the United Nations General Assembly.
Prime ministers of Vanuatu and Solomon Islands called for an investigation into killings and various alleged human rights abuses against West Papuans by Indonesian security forces.
In response, Indonesia's representative accused the countries of being manipulated by Papuans with separatist agendas to exploit the issue of human rights.
A month on, Ms Marsudi said that in the UN all countries were given freedom to express their thoughts.
But she emphasised that Jakarta was pursuing a comprehensive development programme in Papua to improve living standards.
The minister also noted that the Pacific Islands region was an area of key interest in her country's foreign policy and diplomacy.
"At every annual statement of the Foreign Ministry, we emphasise that the South Pacific region is one of Indonesia's foreign policy concerns."
She said that during the last three years, Indonesia's presence and role in the region were evident in the main representative forums such as the Melanesian Spearhead Group and the Pacific Island Forum.
"In addition, when the South Pacific countries were affected by a disaster, Indonesia was one of the countries that sent aid," she said.