The newspaper found that one in five of the country's 15,700 nursing homes were found on the low end of the five-star scale started late during President George W. Bush's term.
The paper's analysis also found in the data that nearly all of the nursing homes awarded one or two stars are owned by for-profit corporations.
"We want to see improvements, but we don't expect a nursing home will jump to a five-star rating within a one-year time period," Medicare's Thomas Hamilton, who spearheaded the rating system's development, told USA Today.
One positive note Hamilton highlighted comparing annual data was the decrease in the number of one-star homes.
Nursing homes that received low scores in back-to-back years house more than 250,000 patients, according to Medicare data the newspaper analyzed. The stars reflect information collected through inspections, complaint investigations and other data from mostly 2008 and 2009.
"The issue is the owners have to take responsibility for the consequences" of poorly performing homes, Larry Minnix, CEO of American Association of Homes and Services for the Aging, told USA Today. He added that the rating system should include data for patient satisfaction.
Medicare spokeswoman Mary Kahn told the newspaper that a one-star nursing home didn't make it a terrible facility. Even those homes must satisfy basic Medicare requirements, she said.
The lowest-rated homes averaged 14 deficiencies per site, the newspaper's analysis found. Those deficiencies can include quality-of-life measures and safety violations.