The operation, which started on May 17, followed a government ultimatum that called for all refugees to return to the Dzaleka refugee camp by April 15, or face enforced relocation.
Government spokesperson Patrick Botha could not say when the operation, which has been criticized by human rights groups, will end.
"We can't give a timeframe as this is a national security matter," government spokesperson Patrick Botha said in an interview.
"We will continue until we are satisfied that all foreigners that have refugee status are returned to Dzaleka," he said referring to the refugee camp in Dowa district, about 60 km away from Lilongwe.
The government has accused refugees of leaving the overcrowded camp without following proper procedures. The round-up operation started in Lilongwe and has been extended to other districts.
Dzaleka, meant to accommodate up to 12,000 refugees, was as of Monday home to more than 50,600 refugees, mainly from the Democratic Republic of the Congo, Burundi and Rwanda, The U.N. High Commission for Refugees [UNHCR] said.
Botha, while acknowledging the camp was overcrowded, denied that Malawi was abusing the rights of the refugees.
"We are conducting this exercise with dignity," he said, adding the exercise involved verifying refugee and resident permit statuses.
The exercise has drawn criticism from the United Nations and local human rights groups.
"We strongly reiterate our call to the authorities to rescind their relocation decision as the existing structures in Dzaleka refugee camp are already stretched to the limit and cannot accommodate more refugees in a dignified manner," Valentin Tapsoba, director of UNHCR's Regional Bureau for Southern Africa, said in a statement issued on Wednesday.
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