Virginia’s health commissioner abruptly stepped down Thursday over new regulations requiring abortion facilities to meet strict, hospital-style building standards that many clinics contend they cannot afford.

Dr. Karen Remley, a pediatrician who since 2008 had helped the state snuff out smoking in restaurants, respond to the swine flu and begin to grapple with the ongoing fungal meningitis outbreak, said she could not “in good faith” implement some aspects of the abortion regulations.

“While this has been the most fulfilling and challenging role I have ever been in, I can no longer in good faith continue my duties as Commissioner,” she wrote in an e-mail to colleagues and professional organizations.

As commissioner, Remley was the governor’s chief adviser on matters of public health, overseeing the Virginia Department of Health, an agency with an annual budget of $621  million and about 4,000 employees.

Her departure provoked an outcry among the medical community and abortion rights groups.

“The fact that she feels so compromised by undue political pressure — it’s stunning,” said Dr. Wendy Klein, an internist and retired Virginia Commonwealth University medical professor who has spoken against the building rules. “It also makes us that much more vulnerable to the social agenda of the McDonnell administration.”

Gov. Robert F. McDonnell (R), who reappointed Remley to the job his Democratic predecessor first hired her for, issued a written statement that thanked Remley for her service but did not address the issue that prompted her resignation.

“As Commissioner, she served two governors from two different parties, and all the citizens of Virginia, with constant professionalism, intellect and dedication,” he said. “She was a tireless public servant, and we will miss her in the Administration.”

Remley’s resignation provided instant fodder in the U.S. Senate race between former governors Timothy M. Kaine, the abortion rights Democrat who first appointed Remley, and George Allen, a Republican opposed to abortion. Just 90 minutes after Remley hit “send” on her resignation e-mail, and three hours before he was to debate Allen in Blacksburg, Kaine was out with an e-mail of his own.

“It’s unfortunate that a political focus on limiting women’s access to health care has prompted her resignation after many years of diligent and faithful service to the Commonwealth,” said Kaine, who has pushed “women’s issues” throughout his campaign.

Allen’s campaign did not respond to a request for comment.

Victoria Cobb, president of the conservative Family Foundation, which has argued that the building standards will protect women’s health, said the timing of Remley’s departure “reeks of political posturing.” She said in a statement that Kaine and President Obama were “desperately trying to wrap themselves around abortion in the misguided belief it will save their campaigns.”

Dr. Maureen Dempsey, the department’s deputy commissioner, will serve as interim commissioner. She is the former director of the Missouri State Department of Health and Senior Services.

“This is not an issue of pro-choice or pro-life, but one of legal opinions that continued to put politics above public health,” Remley said in an e-mail to The Washington Post. Remley has a medical degree from the University of Missouri, Kansas City and an MBA from Duke University.

In her resignation e-mail, Remley signaled support for parts of the new clinic regulations that had been implemented, such as a requirement that they all be inspected and licensed. But she indicated she was troubled by other requirements still being hammered out.

“Unfortunately, how specific sections of the Virginia Code pertaining to the development and enforcement of these regulations have been and continue to be interpreted has created an environment in which my ability to fulfill my duties is compromised and in good faith I can no longer serve in my role,” she wrote.

In 2011, Virginia’s General Assembly voted to regulate abortion clinics like outpatient surgical centers, requiring stricter standards in such areas as infection control, record-keeping and building design. The process of implementing those rules has zigged and zagged ever since.

In a surprise move in June, the State Board of Health gave existing clinics a reprieve on the part of the regulations that clinics said would be financially crippling: architectural standards requiring physical renovations ranging from widening doorways to installing drinking fountains. Although the clinics still had to meet other new standards, the board grandfathered existing clinics when it came to building rules.

But the board reversed course in September after Attorney General Ken Cuccinelli II refused to certify the regulations. Cuccinelli had contended that the panel lacked the authority to grandfather clinics. In a letter to board members, he had also suggested that his office would not defend them in the event of any lawsuits related to the regulations, and that they could be personally liable for legal bills.

That reversal was not the end of debate over the rules, which are winding their way through a review process expected to stretch into next year.