Half of women questioned by the Equality Commission in Northern Ireland believe their career opportunities were negatively affected by having a baby.
About a third reported unfair treatment by employers upon returning to work.
The online survey of 906 women formed part of the commission's first detailed investigation into the issue.
Chief executive Dr Evelyn Collins said the results were "shocking" and discriminating against pregnant women and new mothers was "unacceptable".
"Over one third of the women (36%) who talked to the commission said they had been treated unfairly or disadvantaged because of their pregnancy or because they took maternity leave," she said.
"They believe this affected their finances, their career opportunities, their status at work and their health. This is not acceptable, 40 years after the introduction of legislation in Northern Ireland to provide protection from sex discrimination in employment."
In addition to the survey, the investigation also held focus groups with 57 women across Northern Ireland and spoke to 58 employers.
The type of unfair treatment included being made redundant, overlooked for promotion, unwanted role change, loss of bonuses and negative attitudes.
Issues during pregnancy included problems getting off for doctors' appointments and no health and safety risk assessment.
The women involved in the investigation had a good level of awareness of employment rights but there was a reluctance to take formal action either within the organisation or to an employment tribunal.
The reasons given included too stressful, too costly and possibly career damaging.
However, Dr Collins said it was encouraging that almost half of respondents thought they were treated fairly during their pregnancy and on their return to work.
The majority of firms had policies in place, such as flexible working arrangements, childcare vouchers and return to work incentives, such as phased return and bonus payments.
But some, particularly smaller firms, highlighted the challenges including accommodating flexible working requests and covering absences.
A small number indicated that they subscribe to common negative stereotypes, such as believing pregnant employees and working mothers to be less able or less committed.
The report contains a number of recommendations, including improving access to advice and information for employers and employees, and promoting good practice and policies.
The report - Expecting Equality: a Formal Investigation under the Sex Discrimination (Northern Ireland) Order 1976 - will be launched on Tuesday at a conference in Belfast.
The majority of survey respondents were employed in the public sector while the majority of focus group participants were private sector employees, but similar experiences were reported.