Part of the dispute was settled by the judgement of the International Court of Justice in the Ligitan and Sipadan Case in 2002 and is now awaiting delimitation between the two countries.

Much of the fine-tuning of the border concerned the Jagoi - Stass region in western Borneo, which, after negotiations stalled in 1930, was not yet considered definitive.

The convention states that the eastern end of the border would start at the 4° 10' North latitude,[7] proceeding westward across the island of Sebatik off the coast of Sabah near Tawau town, bisecting it.

[10] On 26 November 1973, a memorandum of understanding was signed between Indonesia and Malaysia for the joint survey and demarcation of their common land border.

Malaysia's 1979 map The continental shelf and territorial sea boundaries beyond the southern terminus of the 1969 and 1970 agreements have not been agreed to.

Indonesia and Singapore signed an agreement in 2009, extending their defined common boundary to a point where the two countries claim was as far westwards as they could go bilaterally.

The map places Pedra Branca, Middle Rocks and South Ledge inside Malaysia's territorial sea.

The 2008 International Court of Justice decision on the sovereignty of Pedra Branca, Middle Rocks and South Ledge should enable the maritime borders between the three countries in this stretch of waters to be determined.

Revision to the 1979 map will be needed with the awarding of Pedra Branca to Singapore and Middle Rocks to Malaysia by the ICJ.

[12] The boundary begins at Point 21 with coordinates 109° 38'.8E 02° 05'.0N (109° 38' 48"E 02° 05'N) off Tanjung Datu at the western extremity of the Malaysia state of Sarawak.

Point 25 is also the eastern terminus of the Indonesia-Vietnam continental shelf boundary which was agreed to by the two countries in 2003, making it the common tripoint of Indonesia, Malaysia and Vietnam.

Indonesia initially rejected the assertion that the islands belonged to Malaysia and both countries brought the dispute to the International Court of Justice.

The court however did not determine the maritime boundary in the surrounding waters and specifically decided that the 4° 10' North parallel which marked the easternmost portion of the Indonesia-Malaysia land border in Sebatik island did not extend to sea to form either the territorial sea or continental shelf border.

[18] The birth of the Indonesia–Malaysia border, or at least the portion for what is today Peninsula Malaysia, can be attributed to the 1824 treaty between Great Britain and the Netherlands which was signed in London on 17 March 1824.

The treaty determined the spheres of influence in the Malay archipelago between the two colonial powers - Great Britain and the Netherlands.

This line of separation between the spheres of influence became the basis of the border between British Malaya and the Dutch East Indies and ultimately, their successor states Malaysia and Indonesia.

On Borneo, the expansion of British and Dutch interests and influence over local sultanates and kingdoms occurred gradually throughout the 19th century.

The northern shore of Borneo saw the British adventurer James Brooke become the Rajah of Sarawak in 1842 and gradually expanded his kingdom to its present shape and size in 1905.

In the southern part of Borneo, the Dutch were negotiating treaties with various sultanates, allowing it to be the dominant colonial power in that portion of the island.

The dispute over the Ambalat block of the Celebes Sea seabed, believed to be rich in mineral resources, continues.

Malaysia however, claimed a stretch of territorial waters and the continental shelf south of the latitude which included the two islands.

The dispute was brought before the International Court of Justice and on 17 December 2002, decided that sovereignty of Sipadan and Ligitan belonged to Malaysia on the basis of effectivités.

Ambalat is an area of the seabed or continental shelf in the Celebes Sea off the east coast of Borneo which is claimed by Indonesia and Malaysia.

Contrary to popular belief, the International Court of Justice decision over the sovereignty of Sipadan and Ligitan did not solve the dispute over Ambalat as it did not include issues concerning the demarcation of the territorial sea and continental shelf boundaries of the two countries in the area.

[23] The dispute started with Malaysia issuing a map in 1979 of its territorial sea and continental shelf which included the Ambalat block.

The map drew Malaysia's maritime boundary in a southeast direction into the Celebes Sea after it leaves the eastmost point on land on Sebatik island.

Indonesia has never officially announced the exact locations of its maritime boundaries but claimed during its arguments in the Sipadan Case that it continued in a straight line along the 4° 10' North latitude after it leaves Sebatik.

Indonesia claimed that it was ready to begin negotiations to determine the border but said that the Malaysians, which relies on its 1979 territorial waters and continental shelf limit map as the basis for its claim in the area, were not ready as they wanted to settle its maritime border with Singapore adjacent to the area first following the International Court of Justice's award of the sovereignty of Pedra Branca to Singapore.

[30] On 13 March 2015, around 17 Indonesians, comprising 10 policemen, four soldiers and three civilians was caught in Malaysia with 12 firearms (eight pistols and four .38 Smith & Wesson revolvers with bullets) was seized from them after they were intruding past and attacked a Malaysian police station on Sebatik Island, Sabah to get a suspected killer whom they alleged have hiding in the police station on the Malaysian side of Sebatik Island.