Unspeakable: The Autobiography was published on Thursday, and includes an account of the bullying allegations made against Mr Bercow in which a number of officials are named.
A statement issued by the Commons media office on behalf of the House Service - the body which employs the Commons staff - said: "In his book, Mr Bercow has chosen to name a number of staff who have never spoken publicly about their experiences or sought to gain publicity as a result."
In the complaint, Lord Lisvane, who was Clerk of the House, alleged staff had been "bullied" and "humiliated" by the former Speaker.
Mr Bercow has consistently denied allegations of bullying from former members of staff in the past.
Responding to Thursday's statement from the Commons, Mr Bercow strongly defended his actions.
A statement said he was entitled to address "unfounded" allegations made by a small but "highly vocal" group of people who were trying to "blacken his name".
It added: "Critics are entitled to air their views.
"What they are not entitled to do is to make unfounded allegations and expect Mr Bercow to say nothing in return.
"t would be odd if Mr Bercow did not comment on their unfounded allegations and the reasons behind them.
"He was advised by speaker's counsel not to do so in detail while he was in office. He is therefore doing so now.
"If the book had not addressed these issues, he would rightly have been accused of serious omission."
Following the publication of the autobiography, a House of Commons spokesperson said: "It is unacceptable to publicly name current or former staff without their prior knowledge or authority, especially for the purpose of financial gain or commercial success."
"House of Commons staff work incredibly hard to enable the effective functioning of our democracy and have a right to expect that their privacy be respected.
"A crucial element of the work of House of Commons staff is to provide confidential, impartial advice to MPs.
"Breaking this confidentiality undermines this important principle and also places staff in a position from which they are unable to respond."
The intervention will be seen as a further setback to Mr Bercow's hopes of gaining a peerage after stepping down last year from the speaker's chair.
Some ministers have, however, said no-one should be given a peerage while they face outstanding allegations of bullying and abuse.
What prompted the House of Commons statement?
In the book, Mr Bercow said the bullying claims dated back to 2010 when, he said, there was an attempt by senior clerks to take over the running of his office.
He said the then clerk of the House Dr Malcolm Jack and his successor Lord Lisvane (then Robert Rogers) had tried to persuade him to replace two of his "loyal" private secretaries in a shake-up of his office.
The officials they wanted to get rid of were "former state school boys" who had not been to university, he said, while Dr Jack was "every inch the ex-public schoolboy".
"In retrospect, I wish that I had known that this pitch by the clerks effectively to run the speaker's office was not the first such attempt," he wrote.
"It was an old ploy and had been rejected by my predecessors.
"The clerks wanted both to exert greater influence and to add to the career opportunities for clerks.
"I should have realised this and rejected it."