The equality commission is calling for the decriminalisation of abortion after a woman was charged with abortion earlier this month.
The woman, who was given a conditional discharge for three years, suffers from mental health issues. She has a small child and was in an abusive relationship, court heard.
The National Commission for the Promotion of Equality said in a statement on Friday that, "tellingly" it was her abusive partner who reported her to the police for carrying out the medical abortion.
Abortion is illegal in Malta under all circumstances.
Having an abortion or helping someone get an abortion is punishable by up to three years in prison.
In its statement, NCPE said it was calling for the decriminalisation of abortion in order to safeguard the rights, health and well-being of women.
"This outrageous case represents the gendered injustices resulting from the blanket criminalisation of abortion in Malta.
"The current law is being used as a means of power and control over women. While noting that the police treated the woman with respect, and that the court handed down a lenient sentence, the fact remains that an abusive partner could trigger criminal proceedings against the woman due to unjust laws criminalising abortion."
The NCPE said women should never be interrogated, dragged to court and face a potential prison term only because circumstances led them to take a personal decision.
Women in vulnerable situations, such as those in abusive relationships, with limited financial means and migrant women, are suffering the worst consequences of abortion criminalisation due to fewer possibilities of travelling abroad and more chances of being reported to the police, it said.
It is estimated that some 400 Maltese women travel overseas to have an abortion and another 200 purchase abortion pills online every year.
The commission also warned that the current abortion laws add to the risks and hardships experienced by such women, perpetuating suffering and social inequality.
"This case also highlights the utmost importance of ensuring that mental health is not excluded from the criminal code amendment tabled in Parliament last year, that will allow the termination of a pregnancy when the woman’s life and health are in danger.
"The circumstances of this case show that mental health can be a major factor impacting the health and wellbeing of women during pregnancy. Women’s mental health is equally important to and inextricably linked to their physical health. Sending a message to the contrary would be incorrect and dangerous."
The government is proposing amendments to the criminal code that would allow for abortions to be carried out in circumstances when a woman's life is at risk or her health in grave danger.
Health Minister Chris Fearne has said he expects the amendments to have gone through all parliamentary stages by the summer recess.