The repatriation agreement is based on a similar initiative by Bangladesh and Myanmar after a previous crackdown on the Rohingya in 1992.
It involves the Myanmar government verifying the identity of refugees who want to return.
But thousands of Rohingya have never had sufficient identification documents proving their residency in Myanmar.
Aid agencies and the UN have called the agreement a farce.
Al Jazeera's Charles Stratford reports.
