Only one-third of 12,565 patients eligible for the drugs got them - even though they were treated at 201 hospitals that had voluntarily enrolled in the American Heart Association's Get with the Guidelines program.
Reasons why so few doctors "got with the program" are unclear.
But the study authors offered some theories, from lack of marketing for the decades-old drugs to concerns about their safety.
The main drug studied, spironolactone, is a water pill that helps prevent kidneys from absorbing too much sodium, which can lead to excess fluid. In heart failure, water often builds up in lungs, blood and tissue because the heart can't pump properly.
The pills studied have been shown to reduce hospitalizations and deaths.
But they also can be hard on the kidneys and when used in the wrong patients, side effects can be deadly - another reason some doctors may avoid them.
The study found that inappropriate use - in patients with signs of kidney trouble or other specific conditions - was uncommon.
The study appears in Wednesday's Journal of the American Medical Association.
Spironolactone is an old generic drug that is not heavily marketed, so doctors may lack promotional material on how to use it, said Cleveland Clinic researcher Nancy Albert, the study's lead author.
Another reason for infrequent use is that the original 2005 American College of Cardiology/American Heart Association guidelines said these drugs "should be considered."
The wording was changed this year to "recommended," after the 2005-2007 study ended, the study authors said.
Dr. Ileana Pina, a spokeswoman for the heart group and professor at Cleveland's Case Western Reserve University, said the results aren't surprising since other reports have shown doctors don't always follow guidelines.
But because these drugs can improve survival, she said the study results should serve as "a call to action" for doctors who treat heart failure patients.
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