The Centers for Medicare & Medicaid Services (CMS) released its star ratings on the Hospital Compare website this week, with many arguing that the controversial system did not accurately reflect the quality of care found in many institutions, especially teaching and safety-net hospitals.

“The new Overall Hospital Quality Star Rating methodology takes 64 existing quality measures already reported on the Hospital Compare website and summarizes them into a unified rating of one to five stars,” Dr. Kate Goodrich, Director of Center for Clinical Standards and Quality Dr. Kate Goodrich said in a blog post on the CMS site.

Before the release of this rating system, there was no ranking system for hospitals by CMS.

The update raised significant pushback from institutions and organizations, especially the American Hospital Association (AHA).

"The new CMS star ratings program is confusing for patients and families trying to choose the best hospital to meet their health care needs," AHA President and CEO Rick Pollack said in a statement, adding that "health care consumers making critical decisions about their care cannot be expected to rely on a rating system that raises far more questions than it answers."

The new CMS system shocked many in the field with the low ratings earned by numerous well-regarded institutions.

"We are especially troubled that the current ratings scheme unfairly penalizes teaching hospitals and those serving higher numbers of the poor," Pollack added. "We are further disappointed that CMS moved forward with release of its star ratings, which clearly are not ready for prime time."

His statement pointed out that a bipartisan Congressional letter — signed by 60 members of the Senate and more than 225 members of the House – had implored CMS to hold off on the release of the rankings until improvements in methodology could be made.

The ratings on hospitals boil down various quality measures ranging from routine care for such medical events as heart attacks and pneumonia, to hospital-acquired infections.

But, CMS's Goodrich noted, “specialized and cutting edge care that certain hospitals provide, such as specialized cancer care, are not reflected in these quality ratings.”

The initial release of the update had been delayed for feedback. But in a March 18 letter to CMS more details were requested on the methodology used by a number of organizations.

Then on July 7, the AHA, along with the Association of American Medical Colleges, America’s Essential Hospitals and the Federation of American Hospitals wrote to CMS Deputy Administrator for Innovation and Quality Dr. Patrick Conway, stating that since the March letter, “The agency provided additional information on how it calculates and assigns star ratings, but far too little information on whether the methodology gives a fair and accurate appraisal of the true quality of care provided in America’s hospitals ... The very fact that some of the nation’s best known hospitals with the highest of ratings on other assessments and that serve large numbers of low-income and complex patients are slated to receive a small number of stars from CMS should make one question the validity and soundness of the methodology.”

For example, CNBC reported that almost all institutions ranked at the top of U.S. News & World Reports “Best Hospital” list did not get 5 stars from the CMS Hospital Compare, including number one rated Massachusetts General Hospital.

In response to the CMS ranking, Mass General's Dr. Elizabeth Mort told CNBC, "I wouldn't hang my hat on this score, one way or the other."

"We're used to getting these different rankings," the senior vice president for quality and safety at the hospital advised. "I'm not in the least surprised that in one we will get the highest-possible rating, and in one we will not ... these methods for the CMS star ratings are vastly different from the methods used by U.S. News."

She also called the government's measurement methodology “significantly flawed," singling out its reliance on 30-day post-discharge "readmission rate," as a particular problem. "It's probably not a very good measure of hospital quality," she said.

University of Pittsburgh Medical Center, which is ranked 14 by U.S. News, earned just a two-star rating from Hospital Compare.

Its spokeswoman Wendy Zellner blasted the CMS methodology in an email, telling CNBC, "UPMC is a 20-plus hospital integrated health system that typically cares for the sickest of the sick across western Pennsylvania. Ten of our 13 hospitals rated by CMS rank at three stars or higher."

"That said, UPMC and many leading academic medical centers across the country have raised concerns about the questionable methodology used in this process, which does not appropriately adjust for patient complexity and socio-economic status," she noted, adding that "this has led to low ratings for many prominent hospitals that provide excellent care.”

Dr. Clay Dunangan, chief clinical officer at BJC HealthCare, the parent of Barnes-Jewish, which U.S. News ranked 11th and the CMS gave just two stars, also took issue with the methodology, stating that "the star rating system is an oversimplification of performance data and isn't very helpful for consumers trying to identify the best provider for their specific health care needs."

The CMS ratings awarded 102 hospitals the coveted five stars, over 900 hospitals, or 20 percent, four stars, 723 hospitals, or nearly 16 percent, two stars, and 133 one star. In addition, 937 earned no rating because they did not report or lacked sufficient data.