The strike was called in response to proposed changes to the civil service compensation scheme that would cut the redundancy entitlement of civil servants by up to a third.
About 60 per cent of the commission's 500 staff are members of the PCS, but only 215 – accounting for 43 per cent of commission staff – actually took part in the strike.
A spokeswoman for the commission said its contingency plans to manage with reduced staffing had been effective. "We worked hard to minimise disruption to our customers and all of our four offices were operational on both days," she said.
The PCS said more than 200,000 civil servants joined the strike nationally. A spokesman for the union said he expected it to announce dates for further strike action on Thursday morning. He said the dates were likely to be later this month.
An overtime ban has also been agreed by the union to run until 6 April to prevent employers from mitigating the effect of the strikes by requiring staff to do extra work.