Liberal supporters of 58-year-old Anna Grodzka said parliament had missed an opportunity to show that Poland was becoming an open-minded society.
"This could have given a signal for Poles that a person from a discriminated minority can occupy such a high-ranking position," said Miroslawa Makuchowska, vice-president of the Warsaw-based Campaign Against Homophobia.
But Ms Makuchowska said some good had come out of the episode. "The more often Anna appears in the media, the more people are getting used to the issue," she added.
A businesswoman with a psychology degree, Ms Grodzka, formerly a man called Krzysztof Begowski, completed her sex change three years ago. She was elected as Poland's first transsexual member of parliament in October 2011.
The deputy speakership would have been a highly visible role, as it involves occasional ceremonial duties.
Asked yesterday what she thought about missing out on the job, Ms Grodzka said: "I regret it."
Her nomination was blocked before lawmakers even had the opportunity to debate Ms Grodzka's potential as a deputy speaker.
A majority of deputies voted against a motion paving the way for her to take up the post.