Police brought the charges after around 50 Muslims gathered to pray on Wednesday on a road in Thaketa township, the site of one of a growing number of raids by Buddhist hardliners on Islamic events.
Two nearby Islamic schools were shuttered in late April after ultra-nationalists complained local Muslims were illegally using them to conduct prayers.
Authorities have said the closure is temporary, but given no timeline for when they may be reopened.
"We feel sorry. This month is important for us," local Muslim leader Zaw Min Latt told AFP, referring to the holy month of Ramadan which began last week.
"We used those schools for prayer for decades. These restrictions have been brought in after more than 60 years."
Local authorities issued a statement saying the prayer session threatened "stability and the rule of law" in the mainly Muslim neighbourhood in the east of Myanmar's commercial capital.
A policeman who asked not to be named confirmed the charges.
Two officers tried to stop AFP journalists from filming when they visited one of the madrassas on Friday.
"It's our mosque as well as our school. We don't know when it will be reopened," Khin Soe, a local resident in his 50s, said as he set off to pray in another part of town.
The case comes as Myanmar's government has been seeking to clamp down on hate speech after a spike in anti-Muslim actions by hardliners from the country's Buddhist majority.
Religious tensions have soared since a group of Rohingya Muslims attacked police posts in Rakhine State in October, sparking a bloody military crackdown that has drawn widespread international condemnation.
Last week Myanmar's top Buddhist authority officially banned the Ma Ba Tha, an ultra-nationalist movement affiliated with firebrand cleric Wirathu, which responded by simply changing its name.
The move came after nationalists this month clashed with Muslims in another Muslim neighbourhood in Yangon, after pushing police to raid a house there in search of illegal Rohingya Muslim hideouts.
