The research, carried out by The Equality and Human Rights Commission in partnership with the Department for Business, Innovation and Skills, found only a quarter (28%) of the 3,000 mums surveyed raised the issue with their employer.
Of the 77% of mums who reported discrimination, only 3% went through their employer's internal grievance procedure and less than 1% pursued a claim to the employment tribunal.
The Equality and Human Rights Commission is calling for the Government to take "urgent action" to stop the equivalent of 390,000 women experiencing negative treatment at work.
"We simply cannot ignore the true scale of the hidden discrimination that working mothers face," Caroline Waters, deputy chair of the Equality and Human Rights Commission said.
"This is unacceptable in modern Britain, and urgent action is needed to ensure women are able to challenge discrimination and unfairness.
"This is why we are calling on Government to look at the barriers working pregnant women and mothers face in accessing justice."
The survey revealed that women who felt they had been discriminated against weren't raising these issues with their employers for a variety of reasons, including the cost of pursuing a claim, fear of negative repercussions at work, lack of information about their rights, and stress or tiredness.
Half of the mothers surveyed said being a mum had a negative impact on their career, work status or job security.
This "negative impact" took the form of not being informed about promotion opportunities, being denied training opportunities, being threatened with dismissal or being put under pressure to hand in their notice.
Among the respondents, 10% of mothers experienced problems when they needed time off for antenatal appointments and 51% experienced negative consequences after approval of a flexible working request.
The researchers also carried out a separate survey of 3,000 employers.
Out of those involved, 70% thought a woman should declare at recruitment stage if they were pregnant, and a quarter thought that it was reasonable to question women at an interview about their plans to have children.
However, 67% of employers had not sought information or guidance on employment issues relating to pregnancy and maternity.
Joeli Brearley, founder of Pregnant Then Screwed said the research highlights how pregnancy and maternity related discrimination is a "systemic problem".
"The statistics are shocking," she told The Huffington Post UK. "But not entirely surprising.
"The burden of certain legislation and cultural, professional and emotional pressures on women mean mothers are often effectively silenced."
Brearley said what is particularly "troubling" about the research is how few women feel empowered to challenge employers and colleagues, even when the law is on their side.
"We need to generate a cultural and social shift as well as reforming legislation," she added.
"Tackling the root causes of discrimination will take serious commitment from the Government, from employers and from campaign groups like Pregnant Then Screwed.
"But let’s make no bones about it, unless we do something to improve this situation then the problem will continue to fester, crushing women’s confidence and stagnating our ability to be both caregiver and bread-winner.
"That’s bad for society, the economy and the working world as a whole."
The Equality and Human Rights Commission is calling for the Government to:
1. Take more effective steps to prevent employers asking during the recruitment process about a woman’s pregnancy or her intention to have children.
2. Explore the feasibility of a collective insurance scheme to support small and medium sized employers to provide enhanced pay and cover for maternity leave, based on a successful model used in Denmark.
3. Make changes to the employment tribunal fee system to ensure that fees are not a barrier to accessing justice for pregnant women and new mothers.
4. Consider increasing the time limit for a woman to bring an employment tribunal case involving pregnancy and maternity discrimination, from three to six months.
Brearley said she is "pleased" with the recommendations made to the government, however she added there is more that could be done.
"In addition to the recommendations, we would also like to see legislation encourage an equal share of the parenting responsibilities," she said.
"Pregnant Then Screwed is campaigning for six weeks paternity leave paid at 90% of the father’s salary, to be taken once the mother returns to work.
"We are also keen to see laws implemented that support flexible working and we would like clearer legislation for those who are self employed or are on temporary contracts."
Brearley said with such a systemic challenge, we cannot expect overnight change.
She added: "If the Government take this report seriously and start to put into motion some of the changes recommended by the EHRC and other campaign groups, then there is hope that in the future fewer mothers will have to endure this kind of treatment."