Julius Kroehl's remains were dug up from a cemetery Thursday with help from the US Embassy.
They are to be reburied alongside US war veterans near the Panama Canal.
The embassy says authorities will also seek to confirm the identity of the remains and establish a cause of death.
Records say he died at age 47 of malaria, but some suspect he was killed by decompression sickness also known as the bends.
Kroehl was buried in 1867, and his grave was only rediscovered in 2005.
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