The Irish authorities have conducted a series of raids on fishing vessels in ports around the country as part of an investigation into the use of undocumented migrant workers.

The Irish police, the Gardai, declined to comment on the operation, saying it was not yet complete. But it is understood from local sources that officers from its immigration unit, together with the Irish navy, the Workplace Relations Commission and the Office of the Revenue Commissioners targeted trawlers in Castletownbere, in County Cork, and Howth in Dublin on Wednesday. They moved on to other key fishing ports on Thursday.

The Guardian understands the operation was undertaken as part of the Santa Marta project – the initiative led by the pope to tackle human trafficking and modern-day slavery. The project has made the exploitation of migrants in the global fishing sector one of its priorities. Local media reported that the raid teams were focusing on the routes used by Asian and African migrant fishermen to enter Ireland.

An emergency taskforce was set up by the Irish government last year to tackle the illegal employment of Asian and African migrants in its fleet. The government said in February it would issue up to 500 specially created work permits for fishermen from outside the European Economic Area (EEA) after allegations that they were being exploited as cheap labour.

Senior figures in the industry had predicted that at least 1,000 work permits would be needed to ensure the protection of all non-EEA fishermen working in the Irish fleet. Only some 160 permits had been applied for by the scheme’s deadline.

Sources said the operation this week was also aimed at checking whether the permit scheme was working. The fishermen’s union, the International Transport Workers’ Federation (ITF), welcomed the police checks, saying its own port visits in recent months suggested some boat owners were still using undocumented labour and refusing to apply for permits for their workers.

The permit scheme requires owners to register, provide a solicitor-backed contract to workers, and pay the legal minimum wage. ITF’s Ireland coordinator, Ken Fleming, said strong enforcement action was needed “to end the widespread abuse of vulnerable fishers by unscrupulous employers”.

Several Filipino workers have used the scheme to regularise their position after years of working in the state illegally. They told us how happy they were to be properly documented and free to visit their families back home and return to work.

However, migrant support groups expressed concern that the raids were focused on immigration breaches rather than labour exploitation. The Migrant Rights Centre Ireland said it has been contacted by several fishermen who had been put on notice to report to immigration authorities following the raids. “No one asked them about their employment conditions or checked for human trafficking. They are targeting those we most need to help rather than unscrupulous owners,” said Gráinne O’Toole, an MRCI coordinator.