Workmen were seen removing the banner on Sunday, almost one year after a former Russian spy and his daughter were poisoned with the Novichok nerve agent in the city.
Very Rev Nicholas Papadopulos, the Dean of Salisbury Cathedral, said: "This was a remarkably stupid thing to do and makes light of the huge personal tragedies involved, and the damage done to the city by the unprecedented nerve agent attacks on Salisbury last year."
The hanging of the flag, described as a "slap in the face" by one local councillor, reportedly took place overnight.
Thankfully it has been removed now - what a stupid stunt - mocking the serious events sadly experienced in Salisbury last year https://t.co/eDUBFhuOT4— John Glen MP (@JohnGlenUK) February 17, 2019
John Glen, is a Christian and the MP for Salisbury.
Jo Broom, Conservative representative for the St Martin's and Cathedral Ward, said: "My initial reaction was just one of shock and sadness that someone would choose to do this at any time, but particularly as we're leading up to the first anniversary of the incident and the city is very much trying to be positive.
"Residents will just be very upset; it's just a little bit of a slap in the face."
Russian flag hung from Salisbury cathedral this morning, but quickly removed before services pic.twitter.com/x22kFYblbh— james mcc (@james1mcc) February 17, 2019
A police inquiry concluded two Russia secret service agents - Alexander Petrovand Ruslan Boshirov - carried on the nerve agent attack by spraying Novichok on Serhei Skripal's front door.
A 44-year-old woman, Dawn Sturgess, died after she came into contact with a perfume bottle used to contain the substance.
Wiltshire Police said: "We are aware of this matter and inquiries are ongoing. It is not a police matter at the moment."
Stay up to date with the latest news stories from a Christian perspective. Sign up to our daily newsletter and receive more stories like this straight to your inbox every morning.