Niger's government has ordered the Arabs, known as Mahamid, to leave the country accusing them of wrongdoing, including theft and rape.
But they insist they are citizens of Niger and "have no other country to go to", after being given five days to leave the country.
The Mahamid also say they will take their case to the United Nations Security Council.
But the BBC's Idy Baraou says the decision to challenge the government's order through the courts may have come too late, as reports from the east of Niger confirm that the authorities had begun rounding Arabs up around Diffa, located some 1,500km from Niamey.
NIGER'S MAHAMID ARABS
Originally nomads from Chad
150,000 live mainly in Diffa State
Many came after 1974 drought
More fled 1980s Chad fighting
Fought against 1990s Tuareg rebellion
Many of the Arabs came to Niger from neighbouring Chad following the 1974 drought in Chad.
Others who were fleeing fighting in Chad arrived in the 1980s. Many have since risen to senior positions in the military, local administration and in business.
The governor of Diffa State, where most of the Mahamid live, told them it was "high time" to pack and return to Chad.
"We have decided, starting today, to expel these nomadic Arab 'Mohamides' to their home countries," Niger's Interior Minister Mounkaila Modi told national television.
"These foreigners have shown no respect to the rights of the natives and they're putting pressure on pastures in this region. We can no longer accept seeing our ecosystem degraded by foreigners."
Mr Modi said the Mahamid possessed illegal firearms and were a serious threat to the security of local communities and that their camels were draining local oases, Reuters news agency reports.
Like the rest of the country, the east of Niger is extremely arid.
It is populated by nomadic cattle herders, whilst the Arabs also own camels. Not surprisingly, one source of the tension between the communities is water.
With the Sahara desert expanding quite quickly there are growing fears that the scarcity of water could spark future problems in many African countries in the region.
The BBC's West Africa correspondent Will Ross says that with the spread of Islam to Africa in the 7th and 8th centuries, Arabs greatly expanded their presence and influence and there are many examples of how the African and Arab cultures have mixed.
For example, some 20% of East Africa's Swahili language comes from Arabic. Arab and non-Arab Africans both had the common goal of opposing European colonialists.
But there have also been areas where the cultures have clashed, one example being Sudan, which has been plagued by conflict between the Arab dominated government in the north and the black African south.
Source: BBCGüncelleme Tarihi: 20 Eylül 2018, 18:16