The group were being held by Mexico's National System for Integral Family Development, or DIF, following a raid by Mexican police on Friday that targeted Lev Tahor - a strict Jewish sect that practices arranged marriages and full-body coverings for girls as young as three.
The sect is estimated to consist of about 200 to 300 people and rejects the state of Israel.
Neither the DIF nor the office of Mexico's Attorney General's office responded to requests to comment on the case.
On Tuesday, Israel's foreign ministry issued a statement about the raid, saying it "took place after Mexican police gathered incriminating evidence against several members of the cult on suspicion of drug trafficking, rape and more."
Mexican police did not respond to requests for comment.
The Israeli statement said two Lev Tahor members were arrested on human trafficking and severe sexual offences.
It added that many of the members were Israeli citizens and that one former member had taken part in the raid in a bid to be reunited with his 3-year-old son who had remained in the sect. The two were reunited and have returned to Israel, the statement said.
Other members of the sect were transferred to the DIF facility.
The Reuters video showed the group overpowering guards and forcing their way out through a door of the compound where they were being held. Those escaping included children and women holding babies.
"They wouldn't let us leave", said David Rosales, a member of the sect, after the escape. "This is a violation of freedom and religious rights."
Videos shared overnight by Mexican media had shown children climbing on the bars of the facility, crying and calling for their families.
Founded in the 1980s by Israeli Shlomo Helbrans, the Lev Tahor practice an austere form of Judaism. Winning admiration from some Jews for its devoutness, the group is condemned by others as a cult-like sect.
Lev Tahor ("Pure Heart" in Hebrew) has faced multiple allegations of kidnapping, child marriage and physical abuse since it was founded in the 1980s.
Earlier this year, two Lev Tahor leaders were sentenced in the United States to 12 years in prison for kidnapping and sex trafficking crimes.
The group has moved countries frequently, including from the United States, Israel, Canada, Guatemala, Mexico and parts of Europe.