The federal government on Friday ordered that all antidepressant drugs be sold with a prominent “black-box” to warn doctors that the medications increase the risk of suicidal thoughts and behavior among children and adolescents, officials announced.

The decision is a reversal of the agency’s long-standing position on the drugs and could significantly alter how they are marketed, prescribed and used.

Controversy has dogged antidepressants such as Prozac for more than a decade, but most psychiatrists have maintained that suicidal thoughts and behavior are the result of patients’ psychiatric illness, not their medications.

At a press briefing Friday, Lester Crawford, acting director of the Food and Drug Administration (FDA), said regulators now know better. Clinical trials showed that children getting drugs had a 4 percent risk of suicidal thoughts and behavior, compared to a 2 percent risk among children getting sugar pills.

“The use of these products causes a statistically significant increase in suicidal thoughts and behavior among children,” he said. Crawford urged physicians to carefully evaluate patients before deciding whether the benefits of the drugs were worth the risks.

“In other words,” added Sandra Kweder, acting director for the Office of New Drugs at the agency’s Center for Drug Evaluation and Research, “these drugs should not be used casually.”

Congressional investigators are looking into whether the FDA played down the risks or erred in not issuing warnings

sooner. Friday’s announcement comes more than a year after investigators first learned of a problem with the antidepressant Paxil, 10 months after British authorities warned physicians not to use the drugs for children, and eight months after an FDA scientist recommended the agency follow the British lead.

Critics have pointed out that the FDA has previously had access to the studies on which Friday’s warnings were based. Agency officials have said that the trials, conducted largely by pharmaceutical companies during the past seven years, did not clearly distinguish suicidal thoughts and behavior from other side effects. They have defended their cautious approach to recent concerns about the risk of suicide as the scientifically appropriate response and argued that re-evaluations of the data were necessary to give confidence in their conclusions.

Psychiatrists have defended use of the drugs because untreated depression can be deadly. FDA officials have repeatedly worried that warnings like the one announced Friday could scare families away from the drugs and deprive sick children of valuable treatment.

Because the available studies on the drugs were not specifically designed to answer questions about suicide risks, evaluating the scientific evidence has been very complicated. Prozac, for example, has been shown effective in treating children’s depression. Friday’s warning suggests the drug might increase suicidal thoughts and behavior among some children and adolescents while simultaneously reducing depression.

The changes take effect immediately, officials said, and patients and doctors should see the new warnings within weeks.