The move has been questioned by a trademark lawyer, who says the symbol's use on a personal Twitter account is unlikely to be an infringement.
The man, who is living in Singapore, was told he was welcome to use a fern image on his account, which has fewer than 60 followers, providing it was "sufficiently different" from NZTE's trademarked version.
He removed it but said he was surprised and amused NZTE had targeted him.
"Surely NZTE have bigger things to worry about than a Twitter user with 55 followers using a certain silver fern image," he said.
"As a New Zealander the silver fern is a symbol of who I am, and I shouldn't have to pick which version of the fern I use for my account."
Ceri Wells, a partner with intellectual property law firm James and Wells, said the stylised image was copyrighted by NZTE as an artistic work.
But using it on Twitter would not necessarily be trademark infringement unless the account was being used to sell goods.
Mr Wells said NZTE had been "vigorously" looking out for any unauthorised use of the symbol. One of his clients, a milk powder exporter, had been warned after put the symbol on its products.
The issue for NZTE was that the symbol could become generic, which would invalidate its trademark.
The Rugby Union was defending its version of the silver fern "very closely" for the same reason, Mr Wells said.
NZTE marketing director Nick Swallow said its silver fern was a registered trademark "and we need to be able to protect it".
"If we don't, we weaken our intellectual property rights, including the ability to enforce more serious commercially-based infringements."
Mr Swallow acknowledged that use by individuals was usually with "the best of intentions".
"When we come across this, we get in touch to explain its status and why it is available only for licensed use.
"Generally we find individuals don't realise it is a registered trade mark and they are happy to comply."
