Thousands of flags started appearing across the UK from summer last year.
The groups responsible have previously said they were motivated by patriotism, which Leffman dismissed.
“We are proud of our diverse communities in Oxfordshire and of being the first county council to be awarded Local Authority of Sanctuary status,” she said.
“We proudly fly the Union Jack and St George’s flags, which are visible symbols of democracy and unity.”
“However, the widespread installation of flags by Raise the Colours is not a sign of patriotism.
“It is an act of intimidation and division that is having a real and damaging impact on our communities.”
The council also added that their teams removing the flags had been subject to abuse and threatening behaviour, which Leffman described as “totally unacceptable.”
“The council has a responsibility to act where behaviour undermines community cohesion and the safe and inclusive use of public spaces,” the council said in a statement.
“That is why we are taking firm action.”
In January, the local authority revealed it had spent more than £15,000 removing flags from lamp-posts and that it cost about £45 to take down a single flag.