ATF agents are losing track of their government-issued firearms, according to a new report, with records showing multiple instances where officers forgot their guns after leaving them on top of cars, in bathrooms and in automobile glove compartments.

The incidents were catalogued in a report Wednesday by the Milwaukee Journal Sentinel. Internal records obtained by the newspaper reportedly show ATF agents had their guns lost or stolen at least 45 times between 2009 and 2013.

But the ATF sharply disputed the report, with a spokeswoman telling FoxNews.com that many of the lost weapons were later recovered.

Spokeswoman Ginger Colbrun said that of the 19 firearms lost -- as opposed to stolen -- between 2009 and 2013, 13 were "recovered shortly after they were reported lost." Further, she said the cases have "significantly declined," with only loss of a firearm reported last year. With nearly 2,400 agents on the force, she noted the percentage of lost or stolen firearms was less than 1 percent.

"ATF has a stringent firearms and weapons policy for properly securing and storing firearms for which its almost 2,400 agents must adhere," she said.

Though most of the lost weapons were handguns, the newspaper reported that at least two were assault rifles. The report detailed two incidents where agents left their guns on the roof of a car. One Illinois agent placed his Smith & Wesson on top of his car while dropping off his children at a soccer game, and drove away. The gun was later found on an off-ramp.

Another North Dakota agent left his gun on his car roof and forgot about it, until his daughter drove the car to a friend's house, according to the article. The gun was never found.

In yet another incident, two boys in Iowa reportedly found an ATF gun in a storm drain. Only then did the responsible agent tell investigators he had misplaced the gun.

According to the report, the ATF has a bigger problem with lost or stolen weapons than other federal law enforcement agencies. The newspaper previously reported on a questionable operation in Milwaukee during which an ATF machine gun was stolen from an agent's truck in 2012. All these incidents are separate from the discontinued Operation Fast and Furious, which allowed hundreds of guns to be sold and carried into Mexico as part of an anti-trafficking sting.

ATF guns are supposed to be stored in "secured, locked locations" when not being carried by the agents. The Journal Sentinel reported that ATF has reduced the minimum punishment for the first-time loss of weapons from three days of unpaid suspension to one day -- supposedly to encourage agents to quickly report such losses.