Iglesia ni Cristo, in English, Church of Christ, has filed a fraud complaint against him for a cancelled concert last New Year's Eve.
The Grammy award-winner performed on Tuesday at a packed concert in Manila but has not applied for the emigration clearance despite repeated notices that it was required.
The 26-year-old R&B artist has been stuck in Manila for a third day after the complaint.
He said he had come back to the city to play the concert to make up for his cancelled New Year's Eve gig.
Brown had been due to perform at the 55,000-seat Philippine Arena, operated by a corporation owned by the Church.
But the organisation claims he cancelled after being paid in full for a 1 million US dollar (£914,000) contract.
Filipino Justice secretary Leila de Lima said state prosecutors will summon Brown for a preliminary investigation into the complaint, but his presence at that stage of the criminal proceedings can be waived.
She said this meant the singer could leave if he applied for clearance, which she added he had not yet done.
"What is important at this point is for him to know that there are criminal proceedings against him at the preliminary investigation level," Ms De Lima said.
"This is a very serious situation and someone needs to be held accountable for mixing my name up in all this," Brown tweeted. "I've done nothing wrong."
Mr Brown was finally given permission to leave on Friday.
It came after he posted a video on instagram, pleading with Barack Obama to intervene. The video was later removed however he did post a farewell message from the airport.