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The conflict has led to the termination of diplomatic relations on 17 September 1963.
After the fall of Sukarno, relations between Indonesia and Malaysia were restored under President Suharto; as both parties agreed to normalise the bilateral relationship and pursued peaceful co-operation and partnership.
The Malays' homes are on both sides of the strait and also on coastal Borneo, while Dayak homelands are both in East Malaysian Borneo and Indonesian Kalimantan.
Some of Indonesian origin ethnic groups such as Minang, Bugis, and Javanese had significant migration to Malaysia and formed significant communities in Malaysia.
Throughout their history the borders of ancient kingdoms and empires — such as Srivijaya, Majapahit, Malacca, Aceh and Johor-Riau — often comprised both modern day countries.
For centuries, the relations, migrations and interactions between Indonesian and Malaysian people have been quite intense, and it is common for Malaysians to trace their relatives in Indonesia and vice versa.
Their national languages; Indonesian language and Malaysian language are closely related and mutually intelligible, both being standardised registers of Malay.
The majority of the population of both nations were of Austronesian ancestry.
These treaties officially divided the archipelago into two: Malaya, which was ruled by the United Kingdom, and the Dutch East Indies, which was ruled by the Netherlands.
Indonesia has an embassy in Kuala Lumpur and consulates general in Johor Bahru, George Town, Kota Kinabalu and Kuching.