F.B.I. agents in every region of the country have mishandled, mislabeled and lost evidence, according to a highly critical internal investigation that discovered errors with nearly half the pieces of evidence it reviewed.

The evidence collection and retention system is the backbone of the F.B.I.’s investigative process, and the report said it is beset by problems. It also found that the F.B.I. was storing more weapons, less money and valuables, and two tons more drugs than its records had indicated.

The report’s findings, based on a review of more than 41,000 pieces of evidence in F.B.I. offices around the country, could have consequences for criminal investigations and prosecutions. Lawyers can use even minor record-keeping discrepancies to get evidence thrown out of court, and the F.B.I. was alerting prosecutors around the country on Friday that they may need to disclose the errors to defendants.

Many of the problems cited in the report appear to be hiccups in the F.B.I.’s transition to a computer system known as Sentinel, which went online in 2012 and was intended to move the bureau away from a case-management system based on paper files. But other problems, including materials that disappeared or were taken from F.B.I. evidence rooms and not returned, are more serious.