More than half of the biodiversity across the archipelago remains unrecorded due to lack of knowledge coupled with poor awareness by local authorities to halt unprecedented destruction of biodiversity.
As of 2010, only 20 of the more than 400 regencies have begun to catalog the species in their area.
"Indonesia is one of the 17 largest biodiversity hotspots on the planet, but we have not recorded most of it," the deputy assistant of biodiversity conservation at the State Environment Ministry, Utami Andayani, told The Jakarta Post.
She said Indonesia was still vulnerable to biodiversity loss, brought about mainly by human population growth, deforestation, illegal trade in plants and animals and human-induced climate change.
"It is difficult for us to complain if other countries exploit our biodiversity for commercial purposes such as medicine because of the lack of data to prove the species are from Indonesia," she said.
She warned that biodiversity loss would pose a significant threat to the country's food security.
The government has long claimed that Indonesia has 12 percent (515 species) of the world's mammal species, the second-highest level after Brazil, and 17 percent (1,531 species) of total bird species, the fifth-highest in the world.
It said that the country was also home to 15 percent (270 species) of amphibian and reptile species, 31,746 species of vascular plants and 37 percent of the world's species of fish.
Biodiversity-related issues are among key environmental matters this year as the UN has named 2010 the International Biodiversity Year.
Indonesia ratified the Convention on Biological Diversity (CBD) in 1994.
The State Environment Ministry was the national focal point for biodiversity issues and has set up a clearing house mechanism to ensure all parties have access to biodiversity information.
Environmental ministers from around the world will gather in Bali next month to discuss biodiversity, among others topics, and its contribution to the Millennium Development Goals (MDGs).
The meeting, organized by the United Nations Environmental Programs (UNEP), will also discuss the economy of biodiversity and ecosystem services, including marine biodiversity.
The Bali meeting is expected to lead to a result echoing the Nusa Dua declaration, which has already been drafted and agreed to by ministers and heads of delegations attending the planned meeting on Feb. 26, 2010.
The deputy minister for environmental damage control at the Environment Ministry, Masnellyarti Hilman, said the Bali meeting would discuss the plan to set up an expert team on biodiversity issues.
"We will negotiate on the establishment of an Intergovernmental Policy Platform for Biodiversity and Ecosystem Service *IPBES* in Bali," she said.
She said Indonesian delegates wanted the IPBES to be placed under the CBD, thus limiting those eligible to be in the team of experts to signatories to the convention.
The US is not party to the CBD.
A number of countries have proposed that the IPBES should be an independent team of experts who would advise the convention on biodiversity issues.
"We will reject any proposition if non-parties to the CBD are included in the IPBES," she said.