Although the Cambridge Health Alliance (CHA), a hospital system affiliated with Harvard Medical School, is in dire financial straits and looking to eliminate up to 300 jobs­ next year, third-year medical students who are enrolled in the alliance’s hospital-training program will not be affected, officials said.

The CHA acknowledge this week that Massachusetts’ pioneering health care reform law has left it with the burden of treating patients without insurance, but without providing adequate reimbursements to the alliance. The CHA has freezed hiring and cut discretionary spending to curb its losses.

Still, the alliance, which includes Cambridge Hospital and two others in the Boston area, will continue to provide on-site training for third-year students at the Medical School as part of the Integrated Clerkship program that it launched in 2004.

“We are classified as a major teaching facility,” said Gordon H. Boudrow, Jr., the CHA’s chief financial officer. “The best part of our mission is the training, and we are not looking to make any changes in that.”

Boudrow added that the CHA’s mission also includes providing health care to the community.

According to Medical School professor David H. Bor, the clerkship program—which receives much of its financial support from the Medical School—is a redesign of the traditional third-year medical curriculum.

“The Cambridge Health Alliance will continue to be a premier setting for the education of health professional students and post-graduate trainees,” said Bor, who is also the CHA’s chief of medicine. “We provide an exceptional setting in which to teach medical students about societal and public health aspects of medicine, cultural competence, increasing access, and reducing disparities.”

The CHA’s financial woes stem largely from the number of uninsured patients it has been treating in the months following the enactment of Massachusetts’ health care reform act last year.

Prior to the law, the CHA was reimbursed by the Commonwealth for the full cost of providing uncompensated services. But Boudrow said that the CHA is now only receiving 60 to 70 cents for each dollar of medical services that it provides.

This reduction has had a significant financial impact on the Alliance in the past year because many low-income residents do not have health insurance despite the state’s efforts to require them to enroll in subsidized programs.

“The Cambridge Health Alliance has not seen this transition in gear,” Boudrow said. “We are still seeing a relatively high percentage of uninsured still coming.”

Massachusetts’ fund for paying for uninsured patients—the Health Safety Net Trust Fund—provides a fixed payment to all the hospitals based on the level of free care the hospital is expected to provide. But an unexpectedly large number of uninsured patients can blow a hole in hospitals’ books if the payment from the trust was assessed at a lower rate.

Boudrow said that funding from the trust has not been adequate for the CHA—the fund’s second largest recipient, behind the Boston Medical Center.

Boudrow said that he feels the problem stems from the fact that the state underestimated the actual number of uninsured patients in the state of Massachusetts.

“We really support the transition and believe that people should have access to care,” Boudrow said. “But the government needs to realize that things don’t just change overnight.”

Jennifer Kritz, a spokeswoman for the state’s Executive Office of Health and Human Services, said that the Commonwealth recognizes the “important role” that the CHA plays in the state’s health care system, and that it will be “working closely” with the hospitals.

—Staff writer June Q. Wu can be reached at junewu@fas.harvard.edu.