Research published by Women's Mental Health Australia on Tuesday reveals almost half of women with endometriosis reported experiencing anxiety.
The findings have uncovered major gaps in Australia's healthcare system, according to chief operating officer Katrina Locandro.
"It's enormous," she told AAP.
"The government's investing a lot in women's health at the moment... and there is a really practical step that they could be taking to reduce that gap."
The findings indicated physical health conditions are associated with poorer mental health.
But the greatest psychological toll is on women living with female-specific physical health conditions, including polyendocrine metabolic ovarian syndrome, which is a broad condition involving a hormone imbalance, irregular periods and ovarian cysts.
Women with that syndrome reported high rates of depression and anxiety; between 1.6 and 2.2 times higher compared to women who did not have the condition.
The disparity also extended to suicide and self-harm rates, reported by 10 per cent of women with polyendocrine metabolic ovarian syndrome and 13 per cent of women with endometriosis, compared to four per cent of women without those conditions.
The research found that one in three women are not seeking help for their mental health issues, often for financial and stigma reasons.
Ms Locandro says every woman attending a government-funded endometriosis and pelvic pain clinic should receive an integrated mental health assessment and support as a standard offering.
"We're not asking the government to build a new system, we're asking it to strengthen an existing one by recognising that women's physical and mental health are inseparable," she said.
Report co-author Bronwyn Graham said embedding integrated mental health assessment and support into existing services would be a game changer.
"Women are being asked to manage two separate journeys, one for their body and one for their mind, and to find their own way between them at the point they are least able to," Professor Graham said.
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