Primary care providers in Massachusetts, who generally receive high marks for screening for physical ailments, only ask their patients about half the time if they are depressed or have other emotional problems, according to a new statewide survey.

Massachusetts Health Quality Partners, a nonprofit organization that measures physician performance, asked nearly 44,000 adult patients whether they had discussed depression, substance abuse, and other mental health issues with their primary care provider during appointments in the previous year. Out of 100 possible points, doctors scored 56 on average last year, a slight improvement over the 2014 score of 53.

With two years of data now in hand, the report marks the first time the organization has focused on mental health screening.

Given that a federal government advisory group recommended last week that all adults be screened for depression as a routine part of health care, the Massachusetts survey shows that “obviously we are not where we want to be,’’ said Barbra Rabson, president of Mass. Health Quality Partners.

“Depression and substance abuse are often overlooked in primary care visits,’’ she said. “Physicians are not as comfortable screening for it. And patients can be really uncomfortable talking about it.’’

The organization questioned 65,000 privately insured patients about their medical care or that of their child, covering 4,000 doctors in 500 medical practices. It reports results for each practice, but not for individual physicians, on its website, www.healthcarecompassma.org.

The organization has surveyed doctors and patients for a decade. In most areas, physician practices earn high scores. For example, doctors report screening 81 percentof patients who should be screened for colon cancer and 96 percent of diabetics for blood sugar problems.

The organization uses a different scale to measure patients’ experiences, including those involving behavioral health. Patients scored doctors 61 out of 100 points as to whether their doctor or someone in the office asked them if they felt “sad, empty or depressed’’; 44 regarding if their provider discussed a personal problem, family problem, alcohol use, drug use, or a mental or emotional illness with them; and 63 as to whether their provider discussed something in their life that caused them worry or stress.

Rabson said it’s important to increase these scores because behavioral health problems can worsen physical illness. Early identification of depression also can increase the effectiveness of treatment and reduce the longterm cost of a patient’s care.

Doctors said there are many barriers to screening patients for depression that practices are working to overcome.

Physicians can be reluctant to ask patients if they are depressed because if the answer is yes, doctors might not have specialists in the practice to manage it, or time to do so themselves. Doctors are being asked to screen for a growing number of conditions, leaving less time for care of a patient’s known illnesses.

Physicians have been “afraid to look under the covers’’ and find a problem they don’t “necessarily have the resources to manage,’’ said Dr. Eric Weil, associate chief for clinical affairs for general internal medicine at Massachusetts General Hospital. “Once you know of a medical condition, you are obligated to manage it. If you don’t have additional resources to manage it, it can be scary. You can be flying solo when you shouldn’t be.’’

Rabson said certain practices have made significant improvements. For example, Shrewsbury Internal Medicine increased its behavioral health score from 45 in 2014 to 62 in 2015; Brigham and Women’s primary care at Newton Corner rose from 63 in 2014 to 79 in 2015; and Chelsea HealthCare Center increased from 48 in 2014 to 62 in 2015.

The Chelsea health center, which is one of 20 primary care practices affiliated with Mass. General, began giving every patient a questionnaire about their emotional health in the last year, Weil said, as have primary care practices across the Partners HealthCare system. Some practices do it online while others have nurses or medical assistants administer the survey.

Patients whose scores raise a red flag have a more in-depth questionnaire which is given by their physician. That can lead to conversations about how to best manage the problem, through stress-reduction techniques, medication, or a referral to a social worker or psychiatrist.

Weil said the screening tool has been eye-opening in his own practice. “There are occasions when I found patients who have had depression where I would have never anticipated it.’’

Liz Kowalczyk can be reached at kowalczyk@globe.com.