UN deputy spokesman Eduardo del Buey said that pressing the policy in Rakhine state, where there have been widespread clashes between Buddhists and Muslims, would infringe "fundamental human rights".
Rakhine authorities say the two-child rule has been reaffirmed in two townships in the state where most people are Rohingya Muslims. The rule was first imposed by Myanmar's military junta.
Del Buey told reporters that the United Nations was aware that Myanmar authorities planned to impose the two-child rule.
"UN human rights mechanisms have previously addressed these issues and called upon the authorities to remove such policies or practices," he added.
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Myanmar's pro-democracy champion, Aung San Suu Kyi, has also criticized the ban which has been fiercely condemned by human rights groups.
Up to 140,000 people -- mainly Rohingya Muslims -- were displaced in two waves of sectarian unrest between Buddhists and Muslims in Rakhine last year.
Myanmar views the roughly 800,000 Rohingya in the country as illegal Bangladeshi immigrants.