LINCOLN, Maine — Miscommunication and a lack of understanding of a new computer financial program caused double reporting and underestimations of revenue that led to a $1.58 million shortfall in this year’s and last year’s town budgets, officials said Tuesday.

The good news, Town Manager Bill Reed said, is that the errors probably won’t cause an increase in the town’s $19.86 tax rate. Instead, town officials will delay several capital projects and improve efficiencies.

In a memo to the Town Council dated Monday, Reed called the “large mistakes that have been unmasked over the past month” a display of “the lack of management’s oversight and a total breakdown of the system.”

“I have asked myself the following question: ‘How could something so huge go undiscovered until someone asked a question to the auditor?’” Reed wrote.

According to Reed, Assessor Ruth Birtz and Treasurer Gilberte Mayo, the errors were:

• A $200,000 double-booking of revenues from the state Business Equipment Tax Exemption and the Maine Homestead Exemption program accounts in the 2011-2012 budget. The double-bookings occurred in former Town Manager Lisa Goodwin’s budget and on Birtz’s tax commitment account sheets.

The error isn’t part of this year’s budget. It was redressed by a $200,000 transfer from the town’s undesignated fund balance a few months ago.

• A $575,000 overestimation of projected revenues in the town’s four Tax Increment Financing accounts listed in the 2012-13 fiscal budget, again caused by double-bookings. This will require town officials to delay several capital projects.

The projected cuts include $200,000 from the town’s street-paving fund and a $100,000 savings that will occur when town officials delay renovating the old Public Works Department garage.

Town officials will also look to save money by improving efficiencies in the rest of the fiscal year.

• An $809,000 underestimation of projected expenses, again caused by double-bookings, in the town’s TIF accounts in the 2011-12 budget. Town officials compensated for the error by reducing the $2.8 million undesignated — or “rainy day” — fund balance to $1.9 million.

Council Chairman Steve Clay was surprised by the budget problems.

“I have no comment at this time because I really don’t know what has happened yet. I just got the information Monday night and I need to look into this further,” Clay said.

Clay and other councilors were briefed on the errors after a special council meeting Monday night at which councilors issued victualers permits and prepared for Election Day.

Councilors expressed mystification at the errors, saying that audits of previous years done by independent auditors found no serious problems.

The errors have at their root misunderstandings of the town’s new computer software put into place more than a year ago and miscommunication among employees, Reed said.

Reed said alerts should have been sounded over a discrepancy between the town’s municipal appropriation — or all the town’s departmental budgets combined — listed in the town budget in July 2011 and the municipal appropriation listed in the town’s certificate of assessment, which was filed with the state in September 2011.

The certificate of assessment listed an appropriation of $4.3 million when it should have listed $5.1 million, Reed said.

“That should have sent a red flag to management to start an evaluation,” Reed said Tuesday.

The town’s new auditor and town workers started discovering the budget misformatting and double-bookings shortly after they found a $200,000 error during their audit of the 2011-12 fiscal budget. The audit began in July. The auditor, Maine Municipal Auditor Services, presented its findings to Reed on Friday.

Reed had first seen indications of problems in the town’s budgeting format shortly after becoming town manager in July, Birtz said. He succeeded Goodwin, who left the job to become Bangor’s city clerk. Goodwin has an unlisted telephone number in Bangor and did not immediately return emails sent Tuesday.

The fact that town finances could absorb the errors without any immediate effect upon taxpayers shows how strong Lincoln’s budget management has been, Reed said.

“The town is very strong financially,” Reed said.

“We would have been in a much better position if this hadn’t occurred but we are still within acceptable rainy day standards,” he added. “I would have rather we still had the $2.8 million [undesignated fund balance], but the town has had very good financial planning in the past and that’s allowed us to weather this problem very well.”