A dozen clerical employes in the Maryland Department of Health and Mental Hygiene are under investigation for allegedly collecting almost $100,000 in fraudulent overtime pay over the past six months, department officials confirmed today.

The employes, all of whom make less than $18,000 a year, could face dismissal if the initial findings of an internal audit are confirmed, officials said.

"I am convinced there are discrepancies in what people say they worked and what they actually worked," said Douglas H. Morgan, the department's assistant secretary for medical care programs.

Morgan said that once the internal investigation is completed, probably next week, department attorneys would determine whether the state would seek restitution of the money and whether there are grounds for criminal charges against the individuals. Department officials would not identify the employes under investigation but confirmed that they work in the invoice processing division of the state medical assistance program.

A department spokesman said "slightly less" than $100,000 of fraudulent overtime had been uncovered in the investigation that began last month.

Officials said they were unsure how much each employe had collected. But one source in the health department, who asked not to be named, said that one of the clerks whose annual salary is about $13,000 had been paid approximately $11,000 in overtime during the period in question.

The medical care programs administration accounts for about half of the health department's annual budget of $1.2 billion, and is responsible for administering the joint federal-state Medicaid program that provides health care to the poor. The employes under investigation process payment claims submitted by doctors and hospitals.

Maryland's Medicaid program has a history of fiscal problems, including an $80 million deficit several years ago, though Health Secretary Adele Wilzack has been credited by legislators for tightening management of the state's largest agency since taking over as secretary in July 1983.

Morgan today said he is convinced that the overtime problem is an isolated one and is not a widespread practice in the 13,000-person department. "It's not everybody," he said. "It's confined to one unit in one large program. There is absolutely no evidence to suggest this exists anywhere else."

The discrepancies came to light when a department auditor cross-checked employe payroll slips with sign-out sheets that record the comings and goings of employes after normal working hours and on weekends. "They found some things that didn't appear to be kosher and the more questions they asked, the more they came up with," said Morgan.

Health department employes who are eligible for overtime compensation may receive it only after the payments are approved by their supervisor. Department spokesman F. DeSales Meyers said today that any administrators who authorized overtime payment for the employes under investigation "will also be questioned" and could face disciplinary action.

The current investigation is the second time in a little over a year that the health department has had to contend with apparently slipshod handling of personnel matters. In 1983, the department's chief hearing examiner was forced to resign, and three of his assistants demoted, after they were found to be practicing law during hours when they said they were working for the state.