As well as core government agencies, the strike involves workers at job centres, border patrols at ports and airports, and courts.
Some MSPs supporting the strike refused to enter Holyrood which continued with ordinary parliamentary business.
Elaine Smith, Labour MSP for Coatbridge and Chryston, said: "PCS's strike today is particularly pertinent on the day George Osborne will outline more austerity measures that will make the rich richer and everyone else poorer.
"The Labour and trade union movement has fought for decades for the rights of workers and we should not now allow current Westminster and Holyrood governments to take those rights away."
Green party co-leader Patrick Harvie said: "SNP ministers have imposed a further real-terms pay cut which, along with increased pension contributions, means yet further raids on the pockets of people working to deliver the public services we all depend on. The Scottish Government likes to blame the UK coalition but the truth is we have the power in Scotland to end this unfair squeeze."