Until now, the biggest unanswered question in the case has been why Sergeant Melgar was killed. But new clues are emerging on that front.

An American service member who knew Sergeant Melgar said he was under the impression that the sergeant had stumbled on some sort of money-skimming scheme involving the Navy commandos. A retired senior enlisted sailor who served in SEAL Team 6 said Sergeant Melgar discovered the scheme and threatened to report the Navy commandos to the authorities. Sergeant Melgar’s suspicions were first reported in the Daily Beast.

Both people spoke on the condition of anonymity because the sergeant’s death remains under investigation. A spokesman for the Naval Criminal Investigative Service, Ed Buice, declined to comment on the homicide investigation.

Special Operations troops from a range of units can earn qualifications that let them recruit sources for intelligence and pay them. These individuals may handle payments from small cash bags up to storage lockers filled with currency.

Cash from funds to pay informants has a way of going missing, military officials said. Skimming money from funds, which in Mali could be as much as $20,000 at any given time, is relatively easy because the service members are often dealing with sources who are illiterate and cannot sign their names to a receipt. This allows an unscrupulous person to create a bogus receipt with the equivalent of an “X” for a signature, military officials said.

One of the first missions to draw broad public attention to the secretive Navy SEAL Team 6 unit was its dramatic rescue in April 2009 of Capt. Richard Phillips after Somali pirates hijacked the Maersk Alabama cargo ship. Snipers from the unit’s Red Squadron shot and killed three of the pirates in a small rescue boat.

The criminal complaint against the surviving pirate, Abduwali Abdukhadir Muse, describes how Captain Phillips gave roughly $30,000 in cash from the safe aboard the Maersk to the pirates, money that soon disappeared. Captain Phillips later recalled leaning against a sack with the money inside on the lifeboat. When Navy personnel searched the lifeboat, all they found were guns, ammunition, cellphones and radios. The Naval Criminal Investigative Service gave the SEALs polygraph tests about the missing money but could never prove where the $30,000 had gone, and the case was closed. No SEAL from that mission is involved in the Mali case.