INDONESIAN President Suharto has cast doubt on the future of a development partnership among Singapore, the Malaysian State of Johor and Indonesia. He asked how it was that Indonesia as a big nation ''still depended on a small nation''. While he did not name that nation it was seen as an obvious reference to Singapore. ''This is certainly not in line with our goal and because of that there has been an emergence in thinking as to how Batam can be developed within the framework of removing that dependence,'' he said. Mr Suharto's remarks came at the end of a tour of Batam Island in Indonesia's Riau province, which has been the key element of the Growth Triangle. In the past, the development partnership has been hailed as a model of regional co-operation. Mr Suharto's surprising statement follows criticism within Indonesia that the Government was giving special attention to Batam at the expense of other areas of Indonesia. Singapore newspapers yesterday carried Mr Suharto's comment, made on Saturday, but led off reports by saying the president acknowledged the benefits derived from the strengths of the three participants. Recent studies by the Indonesian Institute of Sciences concluded that the main beneficiaries of Batam's development were not local people or Indonesians generally but firms controlled by Indonesian Chinese and foreigners from Singapore and other countries. Indonesian officials have privately complained about Singapore's dominance in the project and the ''pushy attitude'' of some Singaporeans, who they say act as if Batam was an extension of the island republic. The Singapore and Indonesian governments and private companies have invested more than US$3 billion in the 415-square kilometre island, a free-trade zone 20 km southeast of Singapore. Batam has 190 km of roads, three seaports and an airport that is being upgraded to accommodate Boeing 747s. More than 50 companies have signed tenancy agreements with Batam Industrial Park, a joint project of government-linked Singapore Technologies Industrial Corp, Indonesia's Salim Group and Jurong Environmental Engineering.