Authorities, who had previously cast doubt on reports of Mohammed's role, now have new information that leads them to believe he killed Pearl, said one U.S. official who spoke on the condition of anonymity. The official declined to detail the evidence.
The U.S. acknowledgment of Mohammed's suspected role was first reported in Tuesday's editions of the Journal.
However, three senior Pakistani officials involved in the Pearl case said Tuesday they could not confirm suspicions that Khalid Shaikh Mohammed was Pearl's killer.
"Many newspapers have been reporting it. We do not have evidence or credible information," said an official with the Pakistani intelligence service, who spoke on condition of anonymity.
A senior Interior Ministry official said that Pakistani investigators had questioned Mohammed about the Pearl case after he was captured in March 2003, but Mohammed never acknowledged any role in Pearl's killing while he was in Pakistani custody. The official also spoke on the condition of anonymity.
A deputy inspector general of police in Karachi, Fayyaz Leghari, who was in charge of the investigation into Pearl's death at the time, also said he was not aware of Mohammed's involvement. "None of the characters who were questioned by us ever mentioned the name of Khalid," he said. "His name never came up."
Pearl, the Journal's South Asia bureau chief, was abducted on Jan. 23, 2002, while working on a story on Islamic militants in Karachi.
Four days later, the Journal and other media outlets received pictures of Pearl with a gun to his head. A group calling itself the National Movement for the Restoration of Pakistani Sovereignty claimed responsibility for the kidnapping and demanded the release from U.S. custody of suspected Taliban and al Qaeda fighters.
In early February, Pakistani police identified Ahmad Omar Saeed Sheikh, an Islamic militant with a history of kidnapping foreigners, as a prime suspect in Pearl's abduction. He was detained and said Pearl was dead.
A Pakistani court has since given Sheikh a death sentence for his involvement in Pearl's killing. He is appealing.
Other people with ties to the Pakistani militant group Lashkar-e-Jhangvi have been arrested in connection with the killing.
Investigators obtained videotapes apparently showing Pearl being killed as his throat was cut. It was unclear from the pictures who killed him. His body was found in May.
Mohammed was captured in Rawalpindi, Pakistan, on March 1. The CIA is interrogating him at an undisclosed location. He is believed to have been among al Qaeda's most senior, and successful, operational masterminds.
Since his detention, U.S. officials have connected him to more and more al Qaeda and associated operations over the last decade.
"We continue to hope that all those responsible for Danny's kidnap and murder are brought to justice," said Brigitte Trafford, a spokeswoman for the Journal, who said the paper had no other comment on the investigation.
By John J. Lumpkin