Councillor Ray Morgon, leader of the council, addressed the issue after receiving numerous messages from residents about displaying the Union Flag or Cross of St George.
Both flags are flown outside the town hall in Romford throughout the year.
Responding to a public letter from Andrew Rosindell MP, Cllr Morgon said: “We have no problem with residents showing their patriotism by flying flags at their homes or in the borough.
“It must be done safely and with respect.”
He added, though, that flags creating health and safety issues, such as blocking road signs, will be taken down.
“We do need to consider road and other users, and if they are in places that obscure signs or constitute a health and safety issue, then they will be removed.
“We will therefore leave our flags flying unless it causes a real problem.”