Members of the political wing of the New IRA clashed with police as they protested in Londonderry on Saturday.
Dissident republican group Saoradh claims Santander has closed the bank accounts of several of its members at the request of MI5.
Similar protests outside the bank’s branches in Belfast and Newry passed off peacefully.
In a statement on behalf of the group read by a masked man in Belfast, it was alleged “countless” republicans’ accounts had been shut.
“It threatens the livelihood of their children and families. What is fair about closing the accounts without giving them answers?” the spokesman said.
“Santander state they are working for people and communities, but they care more about finance and being controlled by foreign governments.
“Direct action against Santander being complicit in MI5 and Crown forces’ targeting of working-class people by freezing their accounts and restricting access will continue until Santander desist and acknowledge their work at the behest of sinister British Crown forces.”
The group claimed four members were arrested in Derry after “brutal assaults by Crown forces”.
In Newry the group said it had handed a letter of protest to the branch manager.
The protests were the latest in a series of stunts staged by the group after intelligence services routed its leadership.
Three weeks ago the group, joined by Derry New IRA chief Thomas Mellon, gathered at the wall of Maghaberry Prison to protest in support of 10 people on remand following the MI5 sting involving agent Dennis McFadden. Four were arrested after clashing with police and setting off fireworks.
Earlier last month Belfast-based Saoradh members joined a picket in Derry to appease a huffing Mellon.
He claims he has been cut adrift by other leaders after the terror gang killed writer Lyra McKee in the Derry last year.