Some 80 prison officers refused to begin their shift at 07:30 GMT, instead holding a meeting, the BBC understands.
They returned to work shortly after 09:00 GMT.
Prison officers are not permitted to strike and could have faced legal and disciplinary action if they had refused to return to work.
There was no industrial action at Northern Ireland's two other jails, Magilligan near Limavady and Hydebank in south Belfast, prison service sources told the BBC.
Staff in Magilligan held a meeting authorised by the prison service and then started work.
Maghaberry Prison, near Lisburn, houses long-term sentenced and remand prisoners, in both separated and integrated conditions.
A Northern Ireland Prison Service spokesperson said some Maghaberry staff had taken "unauthorised action for a short time" on Friday morning, but that the prison regime had since returned to normal.
"Discussions have been taking place in recent months between Northern Ireland Prison Service and Department of Justice senior managers and the trade unions on a 2016 pay award for prison grades," said the spokesperson.
"The minister has met the Prison Officers' Association and advised them that she is in discussions with her ministerial colleague, the finance minister."
Dozens of prison officers at Northern Ireland's high-security Maghaberry prison have delayed starting work in a dispute over pay and conditions.