Foreign ministry official Sujatmiko said the 205 migrants camped at the port of Merak, Java island, since October were being interviewed by the United Nations High Commissioner for Refugees (UNHCR).
He said that in the coming days they would be flown to a "specific place", believed to be a migrant detention facility on Galang island, near Singapore.
"Today the Indonesian government will solve this migrant issue," Sujatmiko told reporters in Merak.
"They can't stay here because it's private property and it's not a proper place for them," he said, adding: "We are not forcibly removing them.
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Most of the Sri Lankans -- many of whom have been living in tents at the port in recent months -- appeared happy to have the chance to meet UNHCR officials, witnesses said.
The migrants have said they are fleeing persecution in Sri Lanka following the end of a civil war pitting ethnic Tamils against majority Sinhalese.
The stand-off, along with a similar situation last year invo