Millions of people in Sudan have joined a general strike called by ​pro-reform groups, shutting down the centre of cities across the country despite a wave of arrests and intimidation​.

The massive shutdown was called to take place on Sunday, the first day of the working week, and is aimed at relaunching an opposition movement battered by a brutal crackdown and forcing the country’s new military leaders to resign.

Shops were closed and streets were empty throughout the capital, Khartoum, and in the neighbouring Omdurman. Four protesters were killed in sporadic violence in the two cities.

The Sudanese Professionals Association, a leading opposition group, said it had called on people to stay home in protest at the deaths of more than 100 people on Monday last week, when security forces violently dispersed a pro-democracy sit-in outside the military headquarters in Khartoum.

“The peaceful resistance by civil disobedience and the general political strike is the fastest and most effective way to topple the military council … and to hand over power to a transitional civilian authority,” the SPA said.

The military took power after ousting the then president, Omar al-Bashir, in April after months of mass rallies. The ruling Transitional Military Council has since refused demonstrators’ demands for an immediate move to civilian rule, instead pushing for a transitional power-sharing arrangement.

Talks between the opposition Declaration of Freedom and Change Forces alliance and the TMC, which took power after Bashir’s departure, ground to a halt last month then collapsed altogether after the raid on the protest camp.

Residents said heavily armed paramilitaries from the Rapid Support Forces were patrolling parts of Khartoum while the regular army has now deployed in some parts of Omdurman.

The RSF, which is largely made up of militias accused of systemic human rights abuses during the war in Darfur, has been blamed for the killings last week. The force is led by Mohamed Hamdan Dagalo – known as Hemedti – who also serves as the deputy head of the TMC.

The Sudan Doctors’ Committee, the medical affiliate of the SPA, said at least three people were killed on Sunday, including a young man who was shot dead by the RSF in Khartoum’s Bahri neighbourhood. The other two died of their injuries after RSF forces beat them in Omdurman, it said.

Activists say that professionals including bankers, doctors, air traffic control staff, pilots, electrical engineers and economists have been targeted by intelligence services in what they say is an obvious attempt to break the strike.

The central bank issued a statement that said it would not go on strike, but many employees stayed away.

“I am on strike along with many other employees at the bank, I think there are [a] few of our colleagues didn’t go on strike but they sold the blood of the martyrs … I don’t care even if they kick me out. God will decide,” one told the Guardian.

The SPA said airport workers and pilots were taking part in the civil disobedience, and posted photos of a deserted Khartoum international airport.

“Dozens of airport workers have been arrested by intelligence and the RSF since Monday. We do not know their whereabouts,” an airport worker said on condition of anonymity, fearing reprisal.

Activists said the total number of people detained by security services in recent days was unclear but was probably in the hundreds.

Two opposition leaders who met the Ethiopian prime minister, Abiy Ahmed, in Khartoum on Friday have been detained, along with an opposition spokesman.

Abiy was in the Sudanese capital to mediate between the TMC and the opposition, which has refused to reopen negotiations.

The internet remains cut off in Khartoum, with other communications significantly restricted.

Sudan’s military leaders have come under increasing international pressure in recent days. The brutal crackdown prompted outrage in the west while the African Union suspended the country and threatened sanctions if there was no swift transition to democracy.

Even Saudi Arabia and the United Arab Emirates appear to be moderating their previous policy of unconditional support for the TMC, after calls to senior officials from counterparts in Washington.

The TMC will be hoping the opposition will not be able to sustain the shutdown for longer than a few days and, if the strike continues, will face a difficult choice: make concessions or intensify repression, risking further isolation and economic difficulties.