Burundi launched a drive Tuesday to register all foreigners, sparking fears among overseas nationals that the scheme could be a pretext for government surveillance.
All non-Burundians in the crisis-hit country will be required to report to border police offices in the coming two months, according to a public security ministry spokesman.
Several foreigners told AFP they feared it was a pretext to track them, and Rwandans said the process could lead to their community being victimised.
But Public Security Minister Alain-Guillaume Bunyoni insisted last month that the move was aimed at granting foreigners a biometric ID card.
Foreign nationals -- who also include people from West Africa including Congolese, as well as Indians -- will be required to attend police stations in person and carry their travel documents.
"We don't know how the police will use this data and with the violence that has already struck the Rwandan community... I think that I will also have to leave he country," said a Rwandan national born in Burundi 40 years ago.
Thousands of Rwandans who lived in Burundi have fled the country since the start of the crisis after several arrests within their community.
Relations between Burundi and Rwanda are at a low ebb, with Bujumbura and the United Nations accusing Kigali of supporting Burundian rebels.
Burundi was plunged into crisis following over President Pierre Nkurunziza's bid for a third term which he went on to win in a July election.
More than 400 people have been killed since the violence erupted in April and more than 240,000 have fled.