Christian Solidarity Worldwide said Myanmar's tactics ranged "from churches in Yangon finding it difficult to obtain permission to renovate their buildings to pastors in Chin State [in western Myanmar] being killed".
But the state run newspaper said the report was part of ongoing efforts by the US to slander the South-East Asian nation.
"The United States has been making accusations against Myanmar while allowing its follower organisations and stooges to distribute wrong data and facts concerning Myanmar's religious affairs," the daily said.
Myanmar, which has been ruled by the military since 1962, is a predominantly Buddhist nation of some 55 million people.
Buddhists account for 89 per cent of the population, while Christians make up 5 per cent and Muslims 3 per cent, according to official figures.
The US issued a report last year accusing the government of infiltrating religious groups' meetings, preventing Buddhist clergy from teaching about human rights and limiting the repair of Christian and Muslim places of worship.