State health officials, in an effort to integrate care in mental health clinics, are changing the regulations for operating clinics that treat New Yorkers suffering from mental illness and substance abuse problems.

Under the new rules, clinics will be able to treat individuals with both ailments, officials said. Previously, burdensome and expensive licensing requirements largely prevented clinics from functioning in the dual capacity.

“That’s a piece system of care,” the commissioner of the state’s Office of Alcoholism and Substance Abuse Services, Karen Carpenter-Palumbo, said.

Health officials estimate that 1.4 million New Yorkers suffer both from mental illness and substance abuse problems. About half are not receiving treatment, and about 10% are being treated for both.

The commissioner of the state’s Office of Mental Health, Michael Hogan, described the changes as “common sense.” He said mental illness and substance abuse are often linked, citing the case of a person with a substance abuse problem whose underlying ailment is depression.

“It really is a vicious cycle,” Mr. Hogan said. “It really is a situation where somebody is dealing with two illnesses.”

The new rule will affect nearly 1,000 clinics that treat patients with metal illness or addiction.

Aiming to help clinics comply with the new rules, the New York State Health Foundation plans to establish a $2 million “center of excellence,” or training model. The foundation also plans to make onetime grants to a number of clinics seeking to implement new services.

“This is a classical technical assistance,” the foundation’s president and chief executive officer, James Knickman, said. “Ironically, the only place you can get integrated service to date is in-patient programs, which are incredibly expensive.”

Officials said they are still ironing out the details of billing and paperwork. But they said the old regulations did not make sense, as a patient receiving counseling for depression could be told to go to a clinic down the street to receive counseling for substance abuse.

“You don’t have to come on Tuesday for your substance abuse care and come back on Thursday for your mental health care,” Ms. Carpenter-Palumbo said. “If you’re there on Tuesday, you’re there for both.”

Mr. Hogan also said he anticipated further changes in mental health services, such as the integration of mental health and primary care.

“We have many steps to getting to a place where, within reason, any common health problem could be treated in the clinic you go into for care,” he said.