Htin Lin Oo, a columnist and former information officer for the opposition National League for Democracy (NLD) party, was arrested in December over a speech in which he urged Myanmar's hardline Buddhists to show tolerance to minorities in the country.
He was jailed yesterday for two years with hard labour for "insulting religion", and the UN rights office said it was "appalled" at the verdict.
The writer "courageously spoke out against the use of Buddhism as a tool for extremism", it said in a statement.
The plight of the persecuted Rohingya Muslims has drawn international attention following the boat people crisis that erupted last month, in which thousands of impoverished Rohingya and Bangladeshi migrants struggled desperately to reach Southeast Asian countries.
Rohingya complain of systematic discrimination and mistreatment by Myanmar's Buddhist-majority government, which refuses to even recognise them as citizens.
Many have been killed in sectarian clashes with Buddhists in recent years, and hardline Buddhist monks have promoted legislation seen as targeting them.
The UN rights office lamented that "rather than prosecuting individuals, who brazenly call for the Rohingya to be killed, for hate speech and incitement to violence, the authorities have jailed a peaceful advocate who dared to question the misuse and manipulation of religion for extremist ends."
UN rights chief Zeid Ra'ad Al Hussein has previously raised Htin Lin Oo's case with the authorities in Myanmar.
His office said he had warned "the country against creating a new generation of political prisoners by jailing people who seek to enjoy the democratic freedoms they were promised in the reforms the country has undergone in the past two years.
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