WASHINGTON — American taxpayers could face the most chaotic filing season in decades as the Internal Revenue Service digs out from a backlog of millions of documents and unanswered calls that accumulated during the longest federal government shutdown in history.

I.R.S. officials briefed congressional staff members on Friday and painted a grim picture of the agency’s operational capacity just days before the start of tax filing season, which begins on Monday. Despite a deal to end the shutdown on Friday, the funding freeze paralyzed large swaths of the agency during the crucial weeks that its staff prepares for its busiest time of year.

The Trump administration ordered 46,000 I.R.S. employees back to work, without pay, earlier this month. That included 26,000 employees who were recalled to ensure that tax refunds continued to be paid and to answer calls.

But only 12,300 of those 26,000 employees showed up, according to congressional aides briefed by the I.R.S. As a result of their absence, five million written correspondences to the I.R.S. have gone unanswered and only 18 percent of calls to the agency’s Automated Collection System reached a representative. Hold times exceeded an hour, according to a document circulated to House staff members on Friday.