Federal prosecutors in Baltimore offered Roy Lee Clay a stark choice.

He could plead guilty to trafficking one kilogram of heroin, and they would recommend a sentence of 10 years. Or, if he asked for a trial, they would invoke his earlier drug convictions from 1993 and 2004 and, if found guilty, he would face an automatic sentence of life without parole.

Mr. Clay, then 47, was one of the rare federal defendants to gamble on a trial, and it proved to be a disastrous decision. The jury convicted Mr. Clay and at his sentencing last August, Judge Catherine C. Blake, of the United States District Court for the District of Maryland, lamented that the mandatory punishment of life without parole seemed “extremely severe and harsh.”

While mandatory sentence laws have frustrated judges and defense lawyers for nearly three decades, calls to revise the laws have surged in the past year. Driven in part by budget concerns as the federal prison population continues to grow, proposals in Congress to restrict lengthy automatic sentences to drug-gang leaders, kingpins and violent offenders have won bipartisan support. In August, Attorney General Eric H. Holder Jr. instructed federal prosecutors to avoid harsh charges for some lower-level drug defendants.

But the outcry goes beyond mandatory sentences and three-strike laws. Using their discretionary power to apply lengthy “enhancements” on top of required terms, critics say, federal prosecutors are strong-arming defendants into pleading guilty and overpunishing those who do not — undermining the fairness and credibility of the justice system.