An investigation by the Equality Commission, which monitors compliance with equality legislation in the Province, reported unfair treatment such as the termination of employment; a change of role and losing out on pay increases.
Equality Commission chief executive Dr Evelyn Collins said the situation was unacceptable.
She said: “Over one-third of the women who talked to the commission about their experiences said that they had been treated unfairly or disadvantaged because of their pregnancy or because they took maternity leave.
“They believe this affected their finances, their career opportunities, their status at work and their health.
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“This is not acceptable, 40 years after the introduction of legislation in Northern Ireland to provide protection from sex discrimination in employment.”
More than 900 mothers working in the private and public sector, with children aged under five, took part in the research.
A significant percentage, 36%, said they believed they had been treated unfairly or disadvantaged as a result of their pregnancy or maternity leave.
They believed that as a female employee they were expected to make a choice between parenthood and a rewarding career path.
Some women reported firms’ failure to consider the risks to health and safety of pregnant employees.
Others said they were overlooked for promotion; a dilution of work responsibilities; were denied training; had changes to working hours; experienced a reduction in bonus payments and were subjected to negative comments.
The findings of the report, Expecting Equality: a Formal Investigation under the Sex Discrimination (Northern Ireland) Order 1976, will be presented at a conference in the Titanic Belfast on Tuesday.
Employers were also invited to share their experiences.
Of those surveyed, most said that they provide support for pregnant employees and new mothers. They referred to policies and practices they had in place including flexible working arrangements, childcare vouchers and return to work incentives such as phased return and bonus payments.
Some employers also identified challenges associated with managing pregnancy, maternity leave and return to work. Difficulties in providing for staff absences were a concern to small businesses in particular.
Dr Collins said: “It is encouraging that almost half the women who responded to this investigation thought their employer had been supportive during their pregnancy, and on their return to work, and we know that there are many employers who want to do their best for their employees, who follow good practice, and have effective policies in place for pregnant members of staff.
“The results of this investigation highlight the need for an increased focus on ensuring that workplaces are fairer for, and more supportive, of pregnant employees and new mothers.
“We have made a number of recommendations in the report, to improve access to advice and information for employers and for employees, to improve employers’ practices and to highlight the economic benefits of utilising and retaining the skills and experience of pregnant workers and new mothers.
“We also want to encourage employers across all sectors to show leadership at a senior level to gender equality and to building an organisational culture that promotes gender equality in the workplace.”