Gov. Susana Martinez, who appointed Torres to the cabinet position, announced the development Monday in a brief statement.
Martinez said Torres' departure will be Oct. 15, and that she would help the governor's staff work on a smooth transition as it searches for a new leader.
Torres, 50, cited personal reasons for her decision to resign from the job that paid $122,500 a year.
"Unfortunately, due to recent personal developments, including the passing of my mother and a heartfelt desire to spend time with my family, it is time to move on," she said.
Martinez said in the statement that she was grateful to Torres for her hard work in leading the Department of Health, which has more than 3,000 employees.
Torres was the target of various insurgencies by at least some of those employees.
A union representing part of the health department's workforce, the Communication Workers of America 7076, started a petition in June seeking Torres' resignation. Among its complaints were low morale and fear among staff members.
Torres also was the target of a website and hotline run by anonymous people.
The site is called "New Mexico Department of Health in Crisis." A recording on the 24-hour hotline said Torres' administration engaged in "bullying, abuse, retaliation and fraud."
Complaints about the Department of Health are not new and not limited to Torres.
She sailed through her state Senate confirmation hearing in March 2011 without a negative word, but longtime legislators roundly criticized the department she took over.
Then-Sen. Kent Cravens of Albuquerque said the Department of Health was infected with cronyism and improper deal-making, but he and other minority Republicans had not been able to do much about it.
"There's a lot of corruption, a lot of money wasted," Cravens said at the time. " . . . A lot of people out there have learned to game the system."
Two Democratic senators, Majority Leader Michael Sanchez of Belen and Peter Wirth of Santa Fe, told Torres she was taking command of a department with a bad history in terms of fairness.
Sanchez said people within the agency told him qualifications for an executive-level job in Valencia County had been rewritten twice to tailor them to a specific person. Wirth appeared with an independent social worker, Gregory Bundrick, who alleged that people in the department wanted to lower the level of care for those with developmental disabilities.
A newcomer at the time, Torres said she had not approved any appointments, including the one that Sanchez said was rigged.
After that hearing, the Senate Rules Committee never returned to any extended discussion about practices or deficiencies in the Department of Health. Cravens resigned from the Senate to become a lobbyist in September 2011, so his allegations of systemic corruption died.
Before joining Martinez's cabinet, Torres worked at the Rio Grande Medical Group in Las Cruces. She previously was with First Step Pediatrics at Memorial Medical Center and in private practice. She also served on the U.S.-Mexico Border Health Commission.
Martinez said Deputy Secretary Brad McGrath would assume the duties of secretary until a replacement for Torres is appointed.
Milan Simonich, Santa Fe Bureau chief of Texas-New Mexico Newspapers, can be reached at email@example.com or 505-820-6898. His blog is at nmcapitolreport.com