A change in the way the federal government identifies doctors for billing purposes is costing some physicians in New York and nationwide thousands of dollars, largely because of a government administrative glitch.

Doctors said their Medicare payments have been delayed — sometimes weeks and months — as they transition to a new identification number required by the Centers for Medicare & Medicaid Services, known as the National Provider Identifier.

One doctor in the Bronx, Dr. Enid Goris, said the government currently owes her $20,000. She recently tapped her children’s savings accounts to pay some bills. “I shouldn’t have ever touched it, but I had no choice,” the 39-year-old physician said. Untangling the problem could take between two and four months, which is time she does not have, she said. “I don’t have any money,” she said. “I have to pay my bills.”

Other doctors shared similar stories: “We have no cash flow,” a private practice physician in Queens, Dr. Arthur Gudeon, said. His office manager has about 200 rejected Medicare claims on her desk, he said. His staff has cut back on ordering office supplies, and he has not taken a salary in nearly four months, he said. “I really have not had much of a choice,” he said.

The National Provider Identifier is intended to consolidate administrative identification numbers among physicians, who previously had multiple identification tags, according to CMS officials. The identifier is a provision of the Health Insurance Portability and Accountability Act of 1996, and the deadline for fully implementing NPI numbers is May 23.

But starting this month, physicians were required to start using their numbers in some form, alone or with their old numbers. A “crosswalk,” or computer program, was designed to recognize the old and new numbers as belonging to one individual as a way of ensuring continuous reimbursement.

The “crosswalk” has failed, according to doctors whose claims were rejected after they applied for their new NPI numbers. Generally speaking, the problems resulted from small errors on their applications that doctors said should have been overlooked, such as a hyphenated last name or a new office suite number.

“If you miss your middle initial, worked for another doctor, moved office… this can stop you in your tracks,” the executive director of the New York State Podiatric Medical Association, Leonard Thaler, said. “It is a national problem.”

In New York, doctors said, the problem was compounded when a local Medicare contractor, Empire Medicare, which processes claims for the federal agency, changed its billing system in February.

“There are some practices who have had to take out loans to meet payroll because they are, for lack of another word, that broke. They need the money that badly,” the ombudsman for the Medical Society of the State of New York, M. Kathryn Robinson, said.

It was unclear how many doctors were impacted by the glitches, she said, but some doctors fared better than others. “Some doctors were able to get it fixed almost immediately or within a couple of days. Some doctors are still trying to get paid,” she said.

Yesterday, CMS officials said the agency was “very sensitive to any provider that’s getting a claim rejected,” but they said the number of rejected claims was small. “They’ve been given a lot of notice before we started rejecting claims,” an agency spokesman said.

Officials said they have deployed teams to the agency’s contractors, which process claims locally, to help handle the new applications and to help correct the enrollment files.

But doctors painted a different story.

“It really is a nightmare,” Mr. Thaler said. He said “dozens and dozens” of podiatrists were feeling the crunch, particularly because individuals who are old enough to qualify for Medicare also tend to develop foot problems as they grow older.

Medicare is the federal government’s insurance plan for people who are 65 or older and individuals who are disabled. Nationwide, there are 40 million Medicare beneficiaries, and in New York, 2.8 million people were enrolled in Medicare in 2006.

“In fairness, CMS did give notice to this, but like anything else, people are very busy and occupied with patient care. The government complicated the problem because it was only recently that the glitches came to light,” Mr. Thaler said. One podiatrist in Brooklyn, Dr. Lawrence Santi, said unless a doctor has significant savings, the bills can add up. “I can’t tell Brooklyn Union Gas to hold up,” he said. “It’s like someone telling you to stay home for six months and you still have to pay your overhead, your supplies, plus your own living expenses.”

In Dr. Santi’s case, his payments were held up nearly a month, at which point Medicare owed him more than $10,000. He said the glitch occurred because his first Medicare identification number, obtained in 1980, was his social security number. This time, he said, he wanted to use his tax identification number for security purposes. Medicare did not recognize that both numbers belonged to him, so it rejected his claims.

He has been paid, but Dr. Santi said the stress took its toll. “Half your thought is on your work, half your thought is on your financial problem,” he said. “It’s frustrating.”

The Bronx physician, Dr. Goris, said she scared off a new patient recently when she started arguing on the phone with a Medicare representative. To save her practice, she said she plans to ask her husband for a loan, or to see if she can borrow money against one of her credit cards. “I have to feed my children,” she said.