After accusing Dr. Mehmet Oz of “fear mongering” for reporting that some brands of apple juice contained high levels of arsenic, ABC News’s senior health and medical editor, Dr. Richard Besser, was forced to concede last week that Oz was right.

In September, the The Dr. Oz show sparked a controversy when it told viewers that it had collected three-dozen samples from five different brands of apple juice in three US cities, sent them to an independent lab for testing, and found that ten contained levels of arsenic higher than 10 parts per billion, which is the Environmental Protection Agency’s allowable limit for drinking water (currently there is no limit for arsenic in apple juice).

Besser fired back immediately, challenging Oz’s assertions in a head-to-head segment on Good Morning America:

Mehmet, I’m very upset about this. I think that this was extremely irresponsible. Putting out this kind of health warning—manufacturing a health crisis based on faulty, incomplete data—this fear mongering, it reminds me of yelling fire in a movie theater. I’m very annoyed about this… You are telling parents that they are poisoning their children and you have absolutely no evidence that they’re doing that.

Besser chastised Oz for measuring total levels of arsenic without differentiating between the harmless, organic variety and the toxic, inorganic variety, and for sending his samples to only one lab without seeking confirmation from others. “No good scientist would ever do that kind of work,” Besser said.

In a second confrontation with Besser later the same day on ABC’s World News with Diane Sawyer, Oz stressed that he wasn’t advising people to stop drinking apple juice and that his concern was not acute arsenic poisoning, which can cause a variety of problems from vomiting to death depending on the size of the dose, but rather chronic, low-level exposure, which can cause cancer, organ failure, circulatory and respiratory problems.

There is no federal limit for arsenic in apple juice, but the Food and Drug Administration (FDA) sent a letter to Oz before his segment aired explaining that it has been testing fruit juices for arsenic, a naturally occurring element, for several years. It tests samples for total arsenic first, and when it finds an amount greater than 23 parts per billion (ppb), it re-tests the sample for its inorganic arsenic content. Its letter claimed that the “vast majority” of samples contained less than 23 ppb.

“The FDA believes that it would be irresponsible and misleading for The Dr. Oz Show to suggest that apple juice contains unsafe amounts of arsenic based solely on tests for total arsenic,” the letter read.

Shortly after Oz’s segment aired, the FDA released the preliminary results of six years of apple juice screening under its Toxic Elements program, posting test results for seventy samples, all of which showed negligible amounts of total arsenic. Toward the end of November, however, the agency acknowledged that it had withheld publication of test results for eight other samples, which were part of the same data set and had concentrations higher than 23 ppb, reaching as high as 45 ppb. At the same time, the FDA also released test results for an additional eighty-two new samples, bringing the total number of samples tested between 2005 and 2011 to a hundred and sixty. Of those, 12 percent exceeded the 10 ppb drinking water standard and 5 percent exceeded the 23 ppb “level of concern” for juices.

An even greater blow to the FDA’s reassurances soon followed. On November 30, Consumer Reports released the results of an investigation which tested eighty-eight samples of five brands of apple juice and grape juice purchased in New York, New Jersey, and Connecticut. It found that 10 percent of the samples had total arsenic levels exceeding the federal drinking-water standard and, more importantly, that most of the arsenic was the harmful, inorganic variety. The investigation also found that 25 percent of the samples had lead levels higher than the FDA’s 5 ppb limit for bottled water.

The investigation prompted Consumers Union, the advocacy arm of Consumer Reports, to call the 23 ppb “level of concern” inadequate, and the group urged the FDA to set a more protective standard of 3 ppb for arsenic in juice and 5 ppb for lead.

For Oz, it was sweet vindication, and for Besser, a moment of humility. The same day that Consumer Reports released its investigation, the two men appeared together on ABC’s World News to clear the air.

“Does it make you mad that you went into battle with incorrect facts from the FDA?” the host, Diane Sawyer, asked her colleague.

“What bothers me the most is that when Mehmet and I spoke before, the information I had from the FDA was incorrect,” Besser admitted, then turned to Oz and put out his hand.

“You were right,” he said.

The FDA told ABC News that as a result of the saga, it is considering setting an arsenic standard for fruit juices and that it had “expanded [its] surveillance activities and is collecting additional data.” It also told Consumer Reports that it is trying to improve its data-reporting procedures, to avoid the confusion caused by its withholding of the eight high-arsenic test results in September.

All parties seem to agree with the FDA’s statement that apple juice is safe to drink and that the concern revolves around long-term exposure to arsenic, the impacts of which still aren’t fully understood. And though Oz deserves credit for standing by his study, there also are lessons to be learned from flaws in his exposé.

The original broadcast did not stress forcefully enough that chronic, not acute, exposure is the issue. It did not differentiate between organic and inorganic arsenic, as it should have. And Oz did engage in some hyperbole, asserting at one point, “We are poisoning our own families.” He later issued a statement acknowledging that he should have said, “We may be poisoning our own families.”

It should also be pointed out that the St. Petersburg Times in Tampa, Florida, conducted a similar investigation of arsenic in apple juice in March 2010, which found that 25 percent of the eighteen samples it paid to have tested exceeded the 23 ppb “level of concern.”

Oz and Consumer Reports spurred a new and greater level of attention to the problem, however. There’s been a wave of coverage in the last week, although some articles, such as one by The Associated Press, made a convincing argument that the high levels of sugar in apple juice are more of a health threat than the trace amounts of arsenic.

Whatever the case, the safety of fruit juices is an ongoing story that journalists should continue to follow, and the public should be thankful for Oz’s tenacious defense of his work in the face of vigorous criticism.

If you'd like to help CJR and win a chance at one of 10 free print subscriptions, take a brief survey for us here.

Curtis Brainard is the editor of The Observatory, CJR's online critique of science and environment reporting. Follow him on Twitter @cbrainard.