However, DUP Councillor Dale Pankhurst hit out saying the flag was not flown from the building until "well after" 11am but before the noon start of the ceremony.
He said the council had been "inundated with complaints" before an official attended and raised the flag.
"Given its significance it should’ve been planned for well in advance," he added.
"I have emailed chief executive Suzanne Wylie requesting a meeting at the earliest convenience to ensure this doesn’t repeat itself. Many within the community I represent were extremely angered, and if it wasn’t for the complaints, it is highly possible there would’ve been no flag raised."
The council took the decision in 2012 to limit the amount of times it flies the flag from City Hall to the government approved designated days. The move sparked widespread protests and violence for months, however, smaller and less frequent protests continue to be held.
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A spokesman for the council said the decision to hoist the flag was taken on a cross-community basis.
"Members of Belfast City Council have agreed to fly the Union flag on designated days, following guidance from the Department of Culture Sports and Media," he said.
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Linfield Supporters Social Club, 1 Jumna Street, Belfast. Community First Wedding Party.
Charlie Butler, Gregg Clarke, William Humphrey MLA, Gareth McKeown Stephen Paul and Ryan McMinn. Pic: Freddie Parkinson Presseye
"May 19 is not a designated day, however following requests from some Members of Council yesterday (Saturday May 19) cross-party support was sought and agreed to fly the flag to mark the Royal Wedding. Staff ensured the flag was flying from before the Royal Wedding ceremony began."