The Tory minister also angered teachers at the NASUWT teachers’ conferences in Birmingham as she urged unions to “be more helpful” and not issue press releases that relay negative news.
The song, released by a teacher's punk rock group, was written in protest at the academisation of schools and the "pressures on teachers".
The song, released on YouTube by media studies teacher Gary Kaye, is called 'Nicky Morgan's Eyes'.
Lines in the song appear to echo teachers and unions in saying the profession's workload is unmanageable and academies are data-driven.
The second verse says: "I'm standing in the playground with a massive bunch of keys, I'm giving them to businessmen who run academies.
"I'm looking at my colleagues and much to my surprise, They all require improvement and then I realise I'm looking through Nicky Morgan's eyes."
Kaye formed the band one weekend with the express purpose of recording a song about the Education Secretary, the Independent reported.
The north Yorkshire teacher told the newspaper that the recent Budget announcement to turn all schools into academies brought it "all to a head."
"You can protest with a frown on your face or you can protest with a smile on your face, and I'd rather do it with a smile," Kaye said.
"But being a teacher is a lot harder now in terms of workload. It's the government's current obsession with data, gathering data.
"The song is about solidarity with teachers."
Members of the public have been in touch in support of the video by Kaye and 'The Enemies' which has been viewed almost 1,000 times.
The song is based on "Gary Gilmore’s Eyes" by The Adverts and released with permission of songwriter TV Smith, according to Schools Week.
The final line of the song is: "Nicky don't need her eyes to see.
"Nicky has parted from reality."