AUGUSTA — A computer problem at DHHS allowed at least 19,000 Mainers who were not eligible for MaineCare to continue to get benefits, throwing budget assumptions into doubt.

Gov. Paul LePage and Health and Human Services Commissioner Mary Mayhew told legislative leaders and members of the Appropriations Committee about the problem Tuesday afternoon.

“We had people who were no longer eligible for MaineCare that were continuing to be covered,” Mayhew said in an interview Tuesday afternoon. “We are doing an analysis to find what the financial implications are.” MaineCare is the state’s version of Medicaid.

She said staff at DHHS was aware of a problem with the bill paying computer system since 2010, but it was not brought to the attention of her and other agency leaders until January.

She said the bill paying computer system could not communicate with the eligibility system, so individuals were not being removed from the billing system after they were determined not to be eligible for benefits any more.

“We have two information systems that were never designed to talk to one another, and so these cases were not properly closed in the claims payment system,” Mayhew said.

She said the agency is looking back through its records to uncover if there are more cases where people became ineligible but the information never got into the bill paying system.

“We need to do a system level comprehensive analysis of what else should we be looking at within this system that is affecting our data, the integrity of our data and our ability to make informed decisions about this program,” Mayhew said.

She said there is no estimate yet of what the problem means to the legislature’s Appropriations Committee, which is working on a Medicaid budget bill for the second year of the two year budget. Lawmakers recently approved an emergency budget bill to pay the bills for this year.

Mayhew said it is likely there are some additional costs in the current budget year, but removal of all of those persons ineligible for coverage should reduce the expected costs of the program in the second year.

She said it will take four weeks to do the analysis and provide dollar amounts to lawmakers.

Leaders and members of the Appropriations Committee were surprised and upset at the problem. Leaders hoped to end this session in the first week in April.

“It’s obviously enormously frustrating to have this computer problem still haunting us,” said Senate President Kevin Raye, R-Perry. “The whole thing with the computer system is just a nightmare from which we are yet to awaken.”

He said it is unbelievable that the computer problems at DHHS continue. He said legislative leaders will be meeting over the next few days “to get our arms around the magnitude of this” and what its implications are for the session. He said it could have an impact on the timing of the session, but refused to speculate on the length on any delay

Rep. Peggy Rotundo, D-Lewiston, the Democratic leader on the Committee, said it will have an impact. She said the panel cannot complete work on a state budget without numbers it can believe are accurate.

“The magnitude of that incompetence is astounding to me,” she said. “One of the things that is particularly disturbing to me is that someone in DHHS knew in January that there was a problem. This is at the same time we were meeting with the commissioner and her staff trying to figure out why we had a shortfall.”

Rotundo said all through the negotiations on the Medicaid budget for 2012 there were questions about the projections from DHHS and that some figures “just didn’t add up” but they were never told of any problems with the computer system.

“As commissioner I own responsibility for this problem,” Mayhew said. “This issue should have been identified and brought to my attention.”

She said there will be accountability for the problems within her staff and the failure to inform her and the Legislature of the problem. She said she is bringing in help from the state Office of Information Technology and the state controller’s office to help in the analysis.