Protesters replaced an Israeli flag flying above Sheffield Town Hall with a Palestinian flag, after scaling the building during a demonstration.
Footage shared on social media showed a man climbing across the roof to remove the banner before throwing it to a crowd of people below.
In a statement South Yorkshire Police said it believed two men had scaled the building on Tuesday evening.
No arrests had been made, the force said, with enquiries "ongoing".
In the footage, shared by Sheffield Online, people can be heard shouting "take it down" and cheering as the Israeli flag was lowered.
Officers attempted to disperse crowds, with two suspects "fleeing the scene" during the "minor disorder".
The incident happened three days after after dozens of armed fighters from Hamas - the Palestinian militant group - crossed into Israel from Gaza in a surprise attack.
The death toll in Israel has reached 1,200 - while more than 900 people have been killed by retaliatory Israeli air strikes on Gaza.
Leader of Sheffield City Council, Tom Hunt, said: "Everyone has the right to safe and peaceful protest but we cannot support the events that took place during the protest outside Sheffield's Town Hall.
"Protesters put themselves and others in serious danger."
'Full review'
The decision to fly the Israeli flag was made after a request from the Department for Levelling Up, Housing and Communities for local authorities to "consider the action", the council said.
It added that the Union flag was put back on the building at 20:00 BST on Tuesday "as always planned" and said the Israeli flag had been handed back to council staff.
They said a "full review" of the incident would take place and "we will look at the security measures that were in place".
The council said the Israeli flag was flown to "show solidarity with the innocent people in that country who face faced appalling acts of terror".
Discussing the actions of those who were on the roof, Mr Hunt added: "We are a city of sanctuary, and this is not what we stand for.
"There are strong feelings about the situation in Israel and Palestine but we ask everyone to show respect and tolerance at this time."
Meanwhile Clive Betts, MP for Sheffield South East, told the OceanNewsUK the incident was "disappointing".
He added: "I absolutely and utterly condemn the Hamas attack on innocent people.
"We have to look for long-term solutions to stop this violence. It's a two-state solution - but we don't seem to get anywhere near it."
