A major consequence of Transmigration to West Papua is the large-scale displacement of the indigenous population from their traditional lands.
According to Clause 17 of Indonesia's Basic Forestry Act of 1967, indigenous people have no right to resist appropriation of their land for transmigrants or industry: "The rights of traditional law communities may not be allowed to stand in the way of transmigration   sites",   and Article 2 of the Basic: Agrarian Law of 1960 says that: "... it is not permissible ... for a community based on its traditional rights, to refuse to allow forest land to be cleared on a large and organised scale for the implementation of large-scale projects undertaken in the framework of plans to increase the production of foodstuffs and to shift the inhabitants" Indigenous people are also likely to receive little or no compensation for lost land. An Indonesian    Minister    for Transmigration has stated "the surrender of land for the needs of transmigration is not accompanied by compensation (ganti rugi)  but  only  by  granting recognition, namely a certificate of recognition of right...
Recognition can take various forms, even the form.of something with no economic value such as the holding of a traditional ceremony, the presentation of agricultural implements, a church or a mosque or other social facilities."   For example, at Arse and other places in the vicinity of Jayapura, the local people have received no compensation for any of the land which they have been obliged to relinquish. Furthermore, if they resist the demand for their land, they may be labelled OPM, which means future military harassment and abuse.
The majority of migrants are from the islands of Java and Sulawesi, but any Indonesian citizen and his family are able to take part in the scheme and receive assistance for transportation and establishment. Most have been resettled in large settlements along the Indonesia/PNG border near the large towns of Jayapura, in the north, and Merauke, in the south (transmigrants now make up over 70% of the urban population of the province) or in the forestry/mining areas of Sorong and Timika.
The  north/south  Trans-Irian Highway will open up to transmigration the previously isolated, and more densely populated, central highlands border area ; a region where a mining concession of over 3 million hectares has been issued by the Indonesian government.
Jakarta's  "Eastward  Development Policy", initiated in 1990, backs both government sponsored and "spontaneous" transmigration, and is planned to industrialise the province.
Transmigration is part of the Indonesian government's stated policy of assimilating indigenous people with the goal of forging a single national identity.
While there are 250 indigenous West Papuan languages, reflecting the isolation and small numbers of many of the language groups, the long term policy of the Indonesian government is the universal use of Bahasa Indonesian, the national language of Indonesia.Bahasa is taught in West Papua's schools from grade one onwards, whereas  in  other  provinces  of Indonesia, the first three years of instruction at primary level are in the vernacular language. Illiteracy in West Papua is nearly double the national average, at 30.5%, and at 810/0 in the highlands.
An overall effect of the influx of immigrant unskilled and skilled labour has been to severely limit opportunities for employment of West Papuans in private sector activities. Unless positive employment policies in favour of the indigenous population are pursued, continued social conflict would appear to be unavoidable.
Radio Australia (June 1997) reported that landowners from the Kwimi, a village 40 km from Jayapura, burned down six new transmigration houses in protest at the government's failure to compensate them for the destruction of a sage tree forest. They had voluntarily given their land,  but demanded compensation for sage trees that would need to be felled.
Transmigration  has  increased pressure on the natural environment in the form of legal and illegal land clearing, and poaching and encroachment by settlers into nature reserves.