He was detained along with the former head of an investment firm, James Hatuikulipi.
The head of the country's anti-corruption commission, Paulus Noa confirmed the arrest to local media but gave no further details.
Another former minister, Bernhard Esau, was also detained at the weekend in connection with the case but was released a day later when a judge said the arrest warrant was invalid. He denies any wrongdoing.
Both Esau and Shanghala resigned as ministers earlier this month when allegations that they had taken bribes in return for fishing quotas emerged.
The Icelandic firm, Samherji is also investigating the allegations.
The two men have not commented on the arrests which dominated the latter stages of the presidential and parliamentary election campaigns.