The two-day talks among 44 countries -- those ravaged by the deadly December 26 tsunamis as well as donors -- along with 14 international organisations, are aimed at allowing regional nations to specify the system they want.
While the technology behind the system will be modelled on the network of seismological centres and tidal gauges already in place in the Pacific, the protocol of who will issue regional warnings was still being thrashed out.
Thailand has proposed hosting a regional centre as part of the new system, which would piggy-back on its Bangkok-based Asian Disaster Preparedness Centre (ADPC), set up by the United Nations in 1986.
It wants to see it paid for via a voluntary trust fund to which the kingdom has already contributed 10 million dollars, with Thai Prime Minister Thaksin Shinawatra calling Friday for countries to match the amount.
But while countries have agreed that the UN's Intergovernment Oceanographic Commission (IOC) should oversee whatever system is chosen, some said more time was needed to consider Thailand's proposal, which was opposed by Indonesia.
"We want a multi-nodal approach, it means not a concept which is hub and spike," Indonesia's ambassador to Thailand Ibrahim Yusuf told AFP.
"We want many national centres divided up -- that would more strengthen the region," he said, noting that Indonesia already has five disaster centres spread across its vast archipelago which could underpin such a system.
Asked whether this meant there would be difficulties producing consensus for a final document among ministers, he said: "Maybe."
Li Baodong, director-general at China's ministry of foreign affairs, also said that differences emerged.
"It seems there are some different opinions but also there is a consensus -- nobody can say we should not strengthen coordination," he told AFP.
"But apart from strengthening coordination, there are different approaches, which will have to be worked out in the rest of the session."
India has also offered to host a regional centre which would be an expansion of its national centre.
Thai Foreign Minister Surakiart Sathirathai said a multi-nodal approach need not conflict with a regional coordination point.
"It seems to me that everyone shares the view that a focal point or regional centre would not preclude the establishment of other cooperation centres in the area," he said mid-way through the talks.
"And then all of these centres would be working together with the (regional) centre that perhaps we establish under the APDC in Thailand," he told reporters.
The executive director of the APDC, Suvit Yodmani, told reporters that at least 10 countries said they would support the centre overseeing the region.
UN Secretary General Kofi Annan said in a message delivered by his special envoy Margareta Wahlstrom that coordination was the next greatest challenge in establishing a system to prevent a repeat of the December 26 disaster, which left more than 280,000 dead.
"Our challenge now is to ensure that all the elements of effective early warning systems are integrated, cohesive and cover not only tsunamis but also other hazards such as cyclones and floods," he said.
The UN's educational, scientific and cultural body UNESCO told the meeting it was instituting an interim alert system ahead of the long-term plan.
"We are planning the installation of six tsunami enabled sea-level stations in the eastern Indian Ocean and the upgrading of 15 more in the whole basin," UNESCO chief Koichiro Matsuura said in a speech read out by a colleague.
The Japanese Meteorological Agency and the IOC Pacific Tsunami Warning Centre could provide information and warnings from their monitoring systems to authorities in Indian Ocean countries, Matsuura said.
Governments and experts say the lack of a warning mechanism was a factor in the high death toll from last month's tsunamis, which hit 11 nations in the region after a massive earthquake off Indonesia.