Laura McNamee, 27, was told by police that she had been threatened by loyalists.
She was co-opted on to the council in 2010 as a replacement for Naomi Long, who won the East Belfast seat from Northern Ireland First Minister Peter Robinson during the general election.
Ms McNamee was identified on social media sites.
An Alliance Party spokesman said: "I can confirm that a threat has been made against her. It was a specific threat identifying her on Facebook. Police have advised her to stay somewhere else."
During Monday night's council meeting it was decided to restrict the flying of the Union flag from 365 days a year to 17. Unionists had wanted no change to the policy while nationalists had called for the complete removal of the flag.
A proposal for designated days was put forward by the non-sectarian Alliance Party and was backed by nationalists.
Ms McNamee accused the UUP and DUP of trying to browbeat Alliance by using scaremonger tactics.
"It has not worked," she told the council chamber.
"The use of the flag as a political football does nothing to support a shared future."