The infighting is so bad that Barbara Bodine, the U.S. ambassador to Yemen has barred the FBI supervisor in the case, John O'Neill, from entering the country and there are currently no FBI agents working the case in Yemen.
The FBI Tuesday acknowledged "friction" between the ambassador and supervising agent, but said it "would not press the case" for seeking his reentry to Yemen.
The State Department, meanwhile, characterized the disagreement as one over how secure Yemen was for FBI agents to do their job.
"When they feel it's comfortable enough for them to go back," said State Department spokesman Richard Boucher, "then I'm sure they will."
In early June, the State Department authorized non-emergency embassy staff and their families to leave the country, urged Americans to postpone trips to Yemen and suspended services to the public at the embassy. Yemeni authorities then arrested at least eight people connected to an alleged plot to bomb the embassy.
FBI agents were pulled out at the same time, because of what the State Department called a "credible threat to their security," but could be related to the interdepartmental feud.
One sticking point in that dispute has been the firearms agents use. Some FBI agents initially were barred by Bodine from bringing assault rifles into Yemen. She wanted the agents to carry only small sidearms.
Bodine was also under pressure from Yemen to limit the number of FBI agents there a point to which some critics say the FBI is insensitive.
"Just as local U.S. officials in the United States bristle when the FBI shows up on the scene, you have the same phenomenon overseas, compounded by the fact that they do not speak the foreign language and they are insensitive from a cultural standpoint by and large," said Larry Johnson, a former State Dept. counterterrorism specialist.
There's also a cultural divide between the FBI and State Department. The State Department uses diplomacy to improve relations, while the FBI aggressively seeks evidence to solve a crime. Rarely do the two approaches go together very smoothly.
The Cole was attacked on Oct. 12, 2000, as it refueled the harbor off Aden, Yemen. Witnesses said a boat laden with explosives drew alongside the Cole and detonated. The blast tore a gaping hole in the destroyer's hull and killed 17 sailors.
A senior Yemeni official said in remarks published last week that Yemen has completed its probe of the bombing of the USS Cole, but has delayed bringing the case to trial at the request of the United States.
Interior Minister Rshad al-Alimi did not say why the United tates was asking for the delay or how long it would be.
Yemen is reported to have arrested a dozen suspects over the attack, but officials say the main one appears to have fled to Afghanistan. Yemeni authorities say eight people have confessed to roles in the bombing.
With some suspects held for eight months, Yemen's government is under domestic pressure including from local human rights groups to bring the case to court. It is against Yemeni law to hold suspects so long without trial.
Yemeni officials have been saying all year they are ready for trial. However, they have held off time and again, apparently as U.S. officials have sought more time for investigators to gather information on others who might have played a role in the attack.
The FBI and Yemeni authorities disagreed early in the Cole probe over what the bureau's role should be in interrogating suspects. The dispute mirrored similar disagreements with Saudi officials during the investigation of the 1996 bombing of Khobar Towers.
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