Chinese experts hailed the initiative for seeking to assimilate religion into a socialist society and as progress for religious development.
In a letter published on its website, the association urged nationwide Islamic associations and mosques to raise national flags all the time and in prominent positions.
Associations and mosques should also study the Chinese Constitution, socialist core values and traditional classical Chinese culture, state-run Global Times quoted the letter as saying.
The legal study classes should be offered so that Muslims can conduct religious activities in accordance with the law and correctly understand its relationship with religious doctrine.
According to an official white paper published last month, China has 20 million Muslims mainly comprised of Uygurs of Xinjiang and Hui Muslims of Ningxia.
Resource-rich Xinjiang home for over 10 million Uygurs was restive during the past few years over resistance to migration of Hans from other provinces.
China blamed the growing incidents of violence on the separatist East Turkistan Islamic Movement (ETIM).
Some internet users questioned whether raising a national flag at a religious site was a violation of the principle of separation of politics and religion, the report sad.
Experts said that Chinese law stipulates that politics and religion should not interfere with each other, but the national flag represents the country, not politics and hanging flags does not intervene in the freedom of religious activities, the report said.
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