One of the women held in the Irwin County Detention Center (ICDC) in Georgia reportedly underwent gynaecological surgery without giving consent and for which she did not receive post-operative care.
The ministry also said that it had identified a second woman who underwent surgery "without her full consent" - or without the procedure or her condition having been explained to her in Spanish.
The contractor that runs the facility says it strongly denies the allegations and any suggestion of misconduct, having been at the centre of controversy since September.
Concerns emerged when nurse Dawn Wooten filed a whistleblower complaint, in which she said she had been told by women inside the detention facility that a number had undergone hysterectomies without giving consent or fully understanding the procedure.
A number of advocacy groups have filed a complaint against the centre on behalf of its detainees, in which they allege medical neglect and poor COVID-19 safety precautions.
According to Project South - one of the organisations which filed the complaint - a former detainee at the centre compared it to a concentration camp, saying: "It was like they're experimenting with our bodies."
Project South had written to members of Congress in 2017, calling for an investigation into the facility's treatment of detainees. In its 2020 complaint, the organisation says "the pattern of lack of medical care and unsanitary conditions at ICDC has only worsened in light of COVID-19".
In an interview with The Intercept, Ms Wooten said that she estimated more than 20 women detained at the centre had undergone hysterectomies in the last six years.
The Mexican foreign ministry has said the first woman it had identified had not undergone a hysterectomy, but did not provide further details on the second.
Ada Rivera is the medical director of the ICE (US Immigration and Enforcement) Health Service Corps.
She said: "According to ICE data, since 2018, only two individuals at Irwin County Detention Center were referred to certified, credentialed medical professionals at gynecological and obstetrical health care facilities for hysterectomies in compliance with National Commission on Correctional Health Care standards.
"Based on their evaluations, these specialists recommended hysterectomies. These recommendations were reviewed by the facility clinical authority and approved."
More than 150 members of Congress have signed a letter to the Department for Homeland Security, which oversees ICE, calling for the claims to be investigated.
The letter states: "We are horrified to see reports of mass hysterectomies performed on detained women in the facility, without their full, informed consent and request that the Office of Inspector General (OIG) conduct an immediate investigation."