In an interview, the former Labour minister told how when she learned of the investigation, which was launched after a confrontation about anti-Semitism with leader Jeremy Corbyn, she "kept thinking what did it feel like to be a Jew in Germany in the Thirties".
Dame Margaret, who has been a vocal critic of Mr Corbyn's handling of anti-Semitism in the party, said that the saga had left her with a "feeling of fear".
Speaking to Sky News, the MP for Barking said: "On the day that I heard that they were going to discipline me and possibly suspend me, it felt almost like, I kept thinking what did it feel like to be a Jew in Germany in the Thirties?
"Because it felt almost as if they were coming for me. It's rather difficult to define, but there's that fear, and it reminded me of what my Dad used to say. My Dad came out of Germany, so he had to leave Germany, he went to Egypt."
She added: "When I heard about the disciplinary action, my emotional response resonated with that feeling of fear that clearly was at the heart of what my father felt when he came to Britain."
Dame Margaret also told how the "cult of Corbynism" had allowed anti-Semitism to bubble to the surface within the party.
She said: "I've never seen it like this, and I think it's a bit scary as well. We've got this sort of growth of populism.
"Whether it's Trump, whether it's Boris Johnson, and now whether it's the cult of Corbynism, which allows these attitudes to emerge and that's what scares me.
"I wasn't alive in the 1930s, there's probably very few people around who were, but it sort of makes you feel if you don't stand up against it then what are you allowing to occur."
Dame Margaret also rounded on Unite boss Len McCluskey, who in a blog accused Jewish community leaders of "intransigent hostility" to Mr Corbyn.
She said: "I find that offensive, I think that's trivialising the issue of anti-Semitism to pretend that somehow we're using that for cheap party political purposes. I'm not, and I think most of those colleagues who are with me, Jews and non-Jewish MPs feel exactly the same as I do."
A Labour Party spokesman, responding to the interview, said: "Jeremy is determined to tackle anti-Semitism in the Labour Party, so Jewish people feel it is a warm and welcoming home.
"The comparison of the Labour Party's disciplinary process with Nazi Germany is so extreme and disconnected from reality it diminishes the seriousness of the issue of anti-Semitism.
"We all need to work together to build support and confidence in the Labour Party among Jewish communities in Britain."