The gang sold more than 200,000 AK-47s, as well as missile launchers and tanks at a time when South Sudan spiralled into civil war, investigators said.
Police said the man was detained on Tuesday along with eight individuals in a coordinated European operation, culminating a four-year inquiry.
His identity and details about who purchased the weapons have been withheld.
A resident on the island of Ibiza who hid behind tight security, the suspect had been posing as an economic adviser to the prime minister of the West African state of Guinea-Bissau and used a fake diplomatic passport, a police spokesman told AFP.
His base in Ibiza was a luxury sea-view villa, with a plaque on the gates that described the site as being consular territory, which thus had diplomatic immunity, they said.
He headed an international network of front firms with links in Belgium, France, Germany and Britain whose headquarters were based in tax havens.
The gang used the firms to procure weapons, notably in Eastern Europe, and a Polish company owned by the suspect acted as a go-between with the buyers, the spokesman said.
The Pole, arrested with eight others, allegedly used the Gambian presidential plane for one of his trips.
He is under suspicion of arms running, money-laundering, tax evasion and extorting millions of dollars from Spanish businesses.
The arrests — part of a joint operation with EU law enforcement agency Europol — coincided with raids in Germany and Switzerland, Spanish police said, adding they had searched several Ibiza residences and impounded a number of luxury cars.
South Sudan became independent from Sudan in 2011, but in 2013 a power struggle broke out between President Salva Kiir and his former deputy, Riek Machar.
The resulting civil war left tens of thousands of people dead.
A peace agreement was reached in August 2015 but the country remains chronically unstable.