The Navy is investigating how thousands of dollars went missing in the rescue of the captain of the Maersk Alabama in April, several news outlets reported Tuesday.

The Naval Criminal Investigative Service opened an investigation into how $30,000 disappeared after special forces snipers shot and killed three pirates, ending the multiday siege and freeing Captain Richard Phillips.

Investigators are talking to anyone who may have had contact with the money or knowledge about what happened to it, a Navy source told CNN, including military personnel on the warship, Navy SEALs who rescued Phillips, and the crew of the Maersk Alabama.

CNN reports that in a criminal complaint filed against the one surviving alleged pirate, Abduwali Muse, the government contends the alleged pirate demanded money from the ship’s captain and led him by gunpoint to the ship’s safe.

"The captain opened the safe and took out approximately $30,000 in cash. Muse and two other pirates then took the cash," the criminal complaint contends.

It goes on to allege that Muse distributed some of the money to the other pirates who retreated to a lifeboat where they were holding the captain as a captive.

The three other pirates were killed by U.S. snipers during the rescue but the complaint does not list any money recovered from the boat after the rescue, CNN reported. It only lists rifles, a hand gun, artillery, cell phones and handheld radios.