The longest government shutdown in history could not have come at a worse time for the IRS, the National Taxpayer Advocate has told Congress.

The IRS was heading into its first filing season under the massive new tax law when the federal government partially closed.

Among the changes was the raising of the standard deduction for married couples to $24,000 from $13,000, and to $12,000 for individuals, from $6,500. Personal exemptions were also eliminated.

"It was the biggest change in 30 years," said Gary Milkwick, chief product officer at 1800Accountant.com, a New York-based tax preparation and consulting firm.

By the time the government reopened in late January, the agency had more than 5 million pieces of mail that had not been processed and 87,000 amended returns waiting to be handled, the report said. The National Taxpayer Advocate is an independent office within the IRS.

At the start of filing season the IRS answered 48 percent of its calls, and the average wait time was 17 minutes. During the same period last year, the IRS answered 86 percent of calls and the average wait time was about four minutes.