The flag had been put in the garden by seven-year-old Anthony's mum Sara Steele for the little boy to enjoy make-believe pirate games.
Sara and her partner, Ronnie Ford-Kennedy were told it had to be removed after a complaint. The angry mum said they were told to take it down it or face court action or a £2,500 fine.
Sara, from Tattershall, Lincs, said: "This is a child's toy. It's sad that someone has reported a child's toy to the council. We don't understand why it constitutes as advertising when it is just a standard pirate's flag in our garden."
Her partner, Ronnie, 42, a former military police officer, said: "Anthony likes playing pirates and when I have my daughters here, they all play pirates together. The flag has been up for three months. I found the letter shocking to say the least."
Anthony has Asperger's syndrome, and his parents say he really does not understand why his flag has to be removed. Ronnie said:
"Anthony has to be told things prior to what is happening because of his syndrome. We've told him we've got to take the flag down, but he doesn't really understand and neither do we. If it just affected me I would not be bothered but this is going to affect a little boy."
His mum Sara added: "Anthony struggles with change and has been quite upset that we need to take the flag down. You can't do anything quickly with him. You have to forewarn Anthony about change otherwise he gets very upset. I think it's utterly ridiculous. It's a child's flag. Who's it hurting?"
The local council insisted it was not planning on taking any formal action against the family, but said it had followed protocol. A spokesman for East Lindsey District Council said:
"The flag flown has been brought to our attention as it is a breach of advertising regulations. As such, and in line with planning law, the district council has written to the family concerned asking that it is taken down.
"Rules around what flags are acceptable are contained within planning legislation and we'd be happy to provide advice and guidance on what is acceptable."
What do you think? Promoting piracy, or, er, complete over-reaction to a child's toy?
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