The flagship BBC programme spoke to dozens of female Westminster employees who work as “clerks” and who made allegations of aggressive and threatening behaviour.
Among those was Speaker John Bercow’s former private secretary, Kate Emms, who left her job in 2011 after less than a year having been signed off sick.
Mr Bercow has rejected the allegations and a spokesman for the speaker said: "Any suggestion to the contrary is simply untrue.”
But colleagues of the former secretary said that Mr Bercow had shouted at her and undermined her in front of other staff which left her unable to continue working in the key Commons post.
Commons authorities were told she suffered from PTSD as a result of these claims.
The Speaker’s spokesperson said: “The Speaker completely and utterly refutes the allegation that he behaved in such a manner, either eight years ago, or at any other time. Any suggestion to the contrary is simply untrue.”
GETTY-BBCBBC Newsnight reveals damning accusations of the Speaker
Some women said they had been pushed against walls, forcibly kissed, groped and slapped by MPs.
They said complaints had not been taken seriously and they fear when complaints are made it is the Clerks who are moved while MPs remain in place.
There is an alleged culture within Westminster that Clerks have to be “tough” and are expected to put up with a lot, according to statements on Newsnight.
Mr Bercow is not the only one accused as two other MPs named in the investigation.
Other MPs accused of bullying are Labour MP for Newcastle-under-Lyme Paul Farrelly and Conservative MP The Wrekin Mark Pritchard.
Witnesses told Newsnight that Mr Farrelly made Clerk Emily Commander’s job impossible.
While recalling his behaviour on a science committee trip to Italy in 2004, one witness said: "He was a complete and utter bully.
GETTY-WIKIPEDIABBC Newsnight: Paul Farrelly and Mark Pritchard were also accused
"He wound her up like a screw and reduced her to tears. The more he upset her, the more he enjoyed it, the more he kept turning the screw.
“He was very aggressive. It felt like no one had the ability or authority to intervene. Everybody knew it was wrong."
The Clerk was also secretary in 2010 when the MP was on the culture, media and sports committee.
Documents obtained by Newsnight show she complained of bullying.
She allegedly told her bosses that she had "repeated nightmares about going on Committee visits with Mr Farrelly and being criticised by him for having neglected tiny details".
Mr Farrelly denies any bullying, telling Newsnight: "In 2012 allegations were made about me having bullied a clerk to the committee during the compilation of the phone-hacking report. These allegations were investigated and not upheld."
GETTYBBC Newsnight: The House of Commons said it does not tolerate bullying of any kind
"Despite this, I apologised if I had inadvertently upset the clerk who had suffered stress. The policy under which they were investigated was considered to be so unfair to those complained about that it was immediately withdrawn and replaced by another policy."
Witnesses told Newsnight that Mr Pritchard had a reputation for shouting and berating Clerks.
Mr Pritchard said: "I understand, over the past several years the House authorities have addressed numerous complaints about MPs, but they have also informed me they have no record of any complaints against me, and if they had, I would have been notified.
The House of Commons said in a statement: "The House of Commons takes pride in being a responsible and supportive employer, and does not tolerate bullying or harassment of any kind."
"In 2014 the House of Commons introduced the revised Respect policy which is specifically designed to combat bullying and harassment of House employees by MPs or their staff.
“In addition, we have implemented a range of measures to complement the respect policy, including training for managers on how to address reports of bullying or harassment and a team of trained bullying and harassment contacts for staff to approach should they have concerns."