Marisela Morales arrived as Mexico's first female attorney general with high marks for bravery.

Secretary of State Hillary Rodham Clinton honored Morales as one of this year's "International Women of Courage," lauding her as a fearless leader in the fight to bring to justice Mexico's most dangerous criminals.

But it will take more than courage if Morales is to succeed as attorney general, one of the most important figures in the government's war against violent drug-trafficking groups, which has killed nearly 40,000 people. Just three months into the job, her efforts have been undermined by the botched prosecution of a high-profile case, highlighting the challenge she faces in a judicial system racked by corruption, inefficiency and inertia.

Morales, a 41-year-old career prosecutor who cut her teeth working gang slayings in Mexico City, is one of the few women of rank anywhere in Mexican law enforcement. The divorced mother had already blazed new paths when she was named the head of Mexico's organized-crime bureau in 2008.

Morales' supporters in Mexico describe a hands-on prosecutor, empathetic and straight as an arrow, and U.S. drug agents here long have talked glowingly of Morales. A leaked U.S. diplomatic cable from 2009 described her ties with American officials as "excellent," in contrast with other Mexican officials who were criticized harshly in the cables and taken to task for failing to wage the drug war effectively.

But Morales has plenty of critics who accuse her of using her legal powers to punish foes of President Felipe Calderon, a conservative.

"She's a puppet," said Leticia Quezada, a leftist congresswoman.

And despite the enthusiastic U.S. backing, Morales sits atop a dinosaur of an agency whose spotty courtroom record and reputation for lethargy make it a weak link in the 4 1/2-year-old drug war.

The agency has had trouble making cases stick. Of 106,320 arrests in 2010 for federal crimes of all types, fewer than 30% resulted in formal charges, according to government figures obtained by the daily Excelsior newspaper this year. The remaining cases were tossed out by judges for lack of evidence.

In the drug war, Mexican forces made more than 82,000 arrests for trafficking between late 2006 and last August, according to official numbers.

But the attorney general's office, known in Spanish as the PGR, does not provide details on how those cases end, making it difficult to judge performance. Part of the problem, analysts say, is that it lacks a modern system for reliably tracking cases and outcomes. Few cases are computerized, for example.

"We have an accountability problem," said Ernesto Lopez Portillo, an expert on Mexican law enforcement. He said the PGR suffers from many of the same problems it did when he was an advisor there in the early 1990s.

Moreover, many specialists agree, the PGR has been weakened by a shuffling of investigative responsibilities as Calderon has focused attention and funds on strengthening the federal police, which has a lead role in the drug fight.

The federal police agency, whose budget is about triple that of the PGR, is led by Genaro Garcia Luna, a canny infighter known for his hyperkinetic pace.The result is an emphasis on arrests and police action, with prosecutions almost an afterthought.

"The PGR is certainly not today what it was 10 years ago," said David Shirk, director of the Trans-Border Institute at the University of San Diego and an expert on Mexican justice. "It has languished."

Wilfrido Robledo, who quit as head of the PGR's investigative police after Morales took over, depicted deep weaknesses as he left. In a leaked report, Robledo, a navy admiral, complained of personnel cutbacks and sagging morale and lamented what he called a "lack of credibility in the institution" as organized crime grew stronger.

Morales and the PGR were humiliated last month when a federal judge threw out weapons charges against former Tijuana Mayor Jorge Hank Rhon, citing lack of evidence.

Suspicions of links to organized crime long swirled around Hank, and his release was seen by many as another failure by the attorney general's office. An editorial cartoon showed Morales, with feet where her hands should be, fumbling a fish bearing Hank's face.

Columnist Carlos Puig proposed scrapping the PGR and starting over, saying it would be "much simpler than trying to reform an abandoned, ill-treated, beaten institution."