Two Namibian government ministers have resigned and the boss of Iceland’s biggest fishing company has stepped aside amid a spiralling scandal over alleged bribes paid to officials in the southern African country in exchange for trawling rights.

Þorsteinn Már Baldvinsson, the CEO of the Icelandic fishing firm Samherji, and Namibia’s fisheries and justice ministers, Bernhard Esau and Sacky Shanghala, are the first heads to roll following revelations this week of a vast corruption case.

Three thousand company documents released by WikiLeaks and investigations by the Icelandic magazine Stundin and the TV show Kveikur showed how Samherji had allegedly paid more than 1bn Icelandic króna (£6.2m) since 2012 to ensure access to the fishing quotas, transferring the proceeds from the catches, mainly of horse-mackerel, via a web of offshore firms to a shell company in the Marshall Islands.

The so-called Fishrot Files suggested Samherji had channelled about £54m to the tax haven in this way between 2011 and 2018, with some of the money reportedly passing through Norway’s largest bank, DNB, in which the Norwegian state holds a 34% stake.

Johannes Stefansson, a former company employee turned whistleblower, told Icelandic media he had approved the kickbacks with Samherji’s backing. The company habitually “does whatever it takes to get its hands on the natural resources of other nations”, Stefansson said.

Iceland’s prime minister, Katrín Jakobsdóttir, said if the allegations against Samherji were true, there was “cause for great concern for Icelandic industrial activity”, adding that the revelations “could affect the nation as a whole”.

As global fish stocks decline, Africa’s coastal waters are becoming more and more sought after by international trawler fleets, with Namibia’s resource-rich fisheries particularly prized. It emerged last year that a fifth of the country’s MPs hold shares in fishing companies.

The country’s media were outraged. The Namibian newspaper spoke of “a coterie of well-heeled vampires sucking the sector dry”, adding that President Hage Geingob, whose Swapo party is seeking to extend its three decades of rule in elections this month, needed to take tougher action.

“No amount of firing of ministers and convicting top officials will fix the looting of state resources, unless loopholes are closed,” the paper wrote. “Corruption is firmly entrenched through laws and policies. It is systemic, and the looters are getting more and more sophisticated to enrich themselves at the expense of ordinary Namibians.”

In Iceland, the fisheries minister, Kristján Þór Júlíusson – a former managing director of Samherji and lifelong friend of Þorsteinn – is facing calls to step aside until investigations into the company’s behaviour are concluded. Halldóra Mogensen, a Pirate party MP, demanded that the minister answer questions in parliament, adding that “the myth of Iceland’s innocence is dead”.

The ruling Independence party, however, blamed a culture of corruption in Namibia for the scandal. “That’s perhaps the root of the problem in this case,” said the finance minister, Bjarni Benediktsson. “A weak government, a corrupt government in this country. That seems to be the underlying problem that we’re seeing now.”