Brown, who's currently on tour with his group New Edition, vacated the New Hope Baptist Church in Newark, N.J., after he was told that the church couldn't accommodate him and his entourage.
Also read: Whitney Houston Funeral: Stevie Wonder, R. Kelly Perform; Kevin Costner Speaks
The Rev. Jesse Jackson, who was in attendance at Houston's funeral, told CNN that Brown and his entourage of "four or five people" took seats in the front row, but were told that the row was reserved for family only. They were asked to move, Jackson said, but there wasn't room at the invitation-only service to seat them elsewhere.
"That was a very difficult moment for all of us; we wanted him to stay," Jackson said. "It seems they could have accommodated him better than they did."
The Rev. Al Sharpton, also in attendance, tweeted from the site that he attempted to keep the peace during the dispute.
"I am at Whitney's funeral. I spoke with Bobby Brown trying to calm him down and not distract from the services," Sharpton wrote. "Today is about Whitney!"
Sharpton softened his stance in a tweet following the funeral.
"We are out of the service," Sharpton wrote. "I don't want anyone distorting Bobby Brown. He has shown love and respect today. Stop hatin'."
Sharpton reiterated his support for Brown to CNN after the funeral, saying, "Bobby did nothing but show love and respect for the memory of Whitney and his daughter … I spoke to Bobby, he said all he wanted to do was show respect and love."
In a statement, Brown said that he was asked to move on three separate occasions, and was prevented from seeing his daughter, Bobbi Kristina, at the funeral.
"I doubt Whitney would have wanted this to occur," Brown's statement reads, according to CNN. "I will continue to pay my respects to my ex-wife the best way I know how."
Brown's tour takes him to Uncasville, Ct., on Saturday night. Coincidentally, the tour will bring Brown back to Newark on Sunday.