The Internal Revenue Service has been having more problems with delayed tax refunds.

Early in tax-filing season, the IRS warned that taxpayers who had filed prior to January 26 might see delays of a week beyond the projected date shown in the online “Where’s My Refund” tool (see IRS Warns of Tax Refund Delays).

However, since February 15, the “Where’s My Refund” tool has displayed a message indicating further delays. “We are aware that some taxpayers who have filed electronically and received an acknowledgement from the IRS are concerned when they visit ‘Where's My Refund’ and are told that we have no information regarding their return,” said an update message on the page five days later. “This is a temporary situation, and we expect to resolve the matter in a few days. At that time, taxpayers will be able to get an expected refund date when they visit ‘Where's My Refund.’”

Part of the problem appears to be with the new filters that the IRS installed this tax season to combat identity theft fraud, and which were blamed for causing the delays last month (see IRS Steps up Efforts to Combat Identity Theft Fraud).

The IRS asked taxpayers not to repeatedly call the agency to inquire about their refunds, but apparently many taxpayers are concerned about the delays, especially when they are getting mixed signals from the “Where’s My Refund” tool.

“If a taxpayer received an acknowledgment message that their e-filed tax return has been received, they can be assured that the IRS has the tax return even though ‘Where's My Refund’ does not reflect that,” said the IRS. “Taxpayers should not call the IRS unless specifically directed by ‘Where's My Refund,’ as there is no new information to give them.”

The IRS apologized to taxpayers for the situation and said most of the refunds would be issued within 21 days. “We expect the vast majority of tax refunds to continue to be issued within the historical range of 10 to 21 days,” said the IRS. “The IRS is taking steps to update information so that Where's My Refund has current information. The IRS apologizes for any inconvenience and will provide updated information as soon as possible.”

The IRS said that most of the delayed refunds were filed between February 2 and February 7, according to a local ABC News affiliate in Charleston, S.C. Other taxpayers were reporting delays of nearly a month, according to eCreditDaily.com.

When the IRS blocked tax refunds last year, the Taxpayer Advocate Service found that 75 percent of the taxpayers who complained to the service ultimately were found to be eligible for the blocked refunds, but taxpayers had to wait an average of nearly six months to receive them (see IRS Fraud Detection System Leads to Refund Delays). The average amount of the blocked refunds was upwards of $5,600.