Arngrimur Brynjolfsonn, described as a former Samherji vessel captain by Icelandic state broadcaster RUV, has been arrested on suspicion of illegal fishing.
The news emerged in reports by the Namibian Broadcasting Corporation (NBC).
Brynjolfsonn appeared in court along with Russian captain Iurri Festison but in separate courtrooms.
A judge ruled that Brynjolfsonn must remain in custody until bail of $100,000 ($90,347) is paid. His lawyers are attempting to secure permission for him to visit his sick wife in Iceland, NBC reported.