"The results have come, it is Daniel's body," the investigator said on condition of anonymity.
Pearl disappeared in the southern Pakistan city of Karachi on Jan. 23 while researching a story for the Wall Street Journal on Islamic militants. A videotape later emerged showing he had been killed.
Meanwhile, British-born Islamic militant Ahmed Omar Saeed Sheikh was sentenced to death Monday for masterminding Pearl's kidnapping and murder while three accomplices were given life in jail. All four have appealed their convictions. Saeed filed an appeal of his sentence on Friday, a defense lawyer said.
His appeal, filed in a court in the southern port city of Karachi, claims the verdict was based upon "fake, false and provenly planted evidence."
Saeed's lawyer, Abdul Waheed Katpar, said the appeal was filed within seven days, as required by law.
"Two high court judges will hear this appeal, and I am 100 percent confident that justice will be done," the lawyer said.
Three other defendants in the case — Salman Saqib, Fahad Naseem and Shaikh Adil — were also convicted in the case on Monday and sentenced to life imprisonment, which in Pakistan means 25 years. They filed appeals on Wednesday.
If the appeals are denied at the provincial level, the men can take their case to the Supreme Court. The process could take more than a year, although the courts are expected to handle this case expeditiously.
Pearl disappeared Jan. 23 in Karachi while researching links between Pakistani extremists and Richard C. Reid, arrested in December on a flight from Paris to Miami with explosives in his shoes.
E-mails received by news organizations a few days later included pictures showing Pearl in captivity. A videotape received by U.S. diplomats in February confirmed Pearl was dead.