Four people have been killed on the first day of a strike, according to doctors aligned to the opposition.
Campaigners have called for ongoing civil disobedience from Sunday to make it as difficult as possible for the military to govern Sudan.
It comes days after a military crackdown left dozens dead.
A number of Sudan's bank, airport and electricity workers were arrested ahead of the strike against the military rule, the main protest group said.
The Sudanese Professionals Association (SPA) said employees were also being threatened by the authorities to scare them into going to work instead of taking part in the nationwide strike.
The ruling Transitional Military Council (TMC) has made no comment.
What is the background?
The military took over Sudan after persistent protests led to the ousting of long-time President Omar al-Bashir in April. They promised a transition to civilian rule.
But pro-democracy campaigners say the military council cannot be trusted after Monday's crackdown against a sit-in demonstration in Khartoum - and they have rejected an offer of talks.
In a separate development, three opposition figures involved in mediation efforts have been arrested.
What's the latest from Khartoum?
Groups of young men have set up barricades in roads as part of the civil disobedience campaign.
Most offices and businesses remain shut and traffic is light in the city, says the BBC's Catherine Byaruhanga in the Sudanese capital.
There have been reports of gunfire as security forces maintain their deployments across most parts of the city.
Protest leaders have asked people to stay at home. They say that demonstrations are no longer possible because of the violent crackdown by the military.
"The civil disobedience movement will begin Sunday and end only when a civilian government announces itself in power on state television," the SPA said in a statement.
"Disobedience is a peaceful act capable of bringing to its knees the most powerful weapons arsenal in the world."