Many Rohingya worry national verification cards will brand them with a permanent immigration status, meaning they can't become full citizens of Myanmar.
Rights groups have criticised the announcement as a publicity stunt and Bangladesh has distanced itself, saying the repatriation was not part of the return process the two countries have been trying to start.
Photos posted alongside the statement showed one man, two women, a young girl and a boy receiving the ID cards and getting health checks.
They are now believed to be staying "temporarily" with relatives in Maungdaw town.
Since August previous year, more than half a million Rohingya have undertaken perilous journeys to Bangladesh to flee persecution and violence in Myanmar.
An estimated 687,000 Rohingya are now living in refugee camps in Bangladesh.
Myanmar and Bangladesh agreed in January to complete a voluntary repatriation of the refugees in two years.
Andrea Giorgetta from the International Federation for Human Rights (FIDH) criticised the repatriation announcement as "a public relations exercise in an attempt to deflect attention from the need for accountability for crimes committed in Rakhine state".
Asif Munier, an independent researcher on migration and refugee, said Myanmar's unilateral action and the efforts to manipulate the issue by portraying it as "repatriation" could undermine the bilateral deal signed in November.
The agency said that in the absence of a tripartite agreement between UNHCR, Myanmar and Bangladesh, The UN agency has continued to engage with governments of both the countries in negotiations on two separate agreements meant to ensure that any future returns are conducted in line with the worldwide standards of voluntariness, safety and dignity.
Around 700,000 Rohingya are trapped in makeshift refugee camps like this one near Cox's Bazar in Bangladesh.
The foreign ministry is not ready to discuss it or take it into consideration because the issue is not related with the repatriation of the hundreds of thousands of Rohingyas who took shelter in Bangladesh after fleeing military crackdown in Rakhine State, the official said. Many refuse to return without a guarantee of basic rights and citizenship.
Hundreds of thousands of Rohingya fled Myanmar's Rakhine State to refugee camps in Bangladesh following violence in August which the United Nations has labelled ethnic cleansing.
Doctors Without Borders says the violence claimed at least 6,700 Rohingya lives in the first month alone.
The statement said authorities determined whether they had lived in Myanmar and provided them with a national verification card.
The move comes despite warnings from the United Nations and other rights groups that a mass repatriation of Rohingya would be premature, as Myanmar has yet to address the systematic legal discrimination and persecution the minority has faced for decades.
Although the Rohingya have lived in Myanmar for many generations, most people in Myanmar consider them unwanted immigrants from neighboring Bangladesh and refer to them as "Bengalis", a term the Rohingya consider derogatory. And a United Nations report from last week says the country still hasn't addressed the actual cause of the crisis. Rahim said the group presented 13 demands for the government to meet for their return to Myanmar.