Hundreds of people have turned out in Khartoum for the first demonstrations since security forces attacked a protest camp in the Sudanese capital last week, killing at least 100 people and injuring many more.

The latest protests came after Sudan’s military rulers admitted that security forces had committed abuses during the attack on the camp. They appear to have been spontaneous as frustration grows after opposition leaders called off a general strike intended to force the generals to agree a transition to civilian rule.

Ahmad Mahmoud, who took part in the earlier Khartoum protests, said he had wanted the civil disobedience campaign to continue until the military leaders gave up power. “People went on strike based on that understanding and then the [opposition leaders] abruptly changed their mind,” he said.

In Omdurman, which sits on the opposite bank of the Nile to Khartoum, hundreds of people protested on Thursday night chanting slogans demanding a civilian government and pledging “a revolution forever”.

“We will continue taking to the streets until we get a civilian government,” Huda El-Fatih, a member of the neighbourhood committee in Wad-Nubawi said.

The grassroots protests pose a significant threat to Sudan’s new regime. The neighbourhood committees have been the backbone of the opposition movement since mass rallies against the autocratic 30-year rule of the former president Omar al-Bashir began in December last year.

The military ousted Bashir in April after tens of thousands of protesters set up a camp in the centre of Khartoum. The country has been ruled by the Transitional Military Council (TMC) ever since.

A protester in Shamabat Bahri in the north of Khartoum who refused to give her name for fear of reprisals, said she had been furious after listening to the “lies of the TMC”.

“We chanted for a civilian government, and we went to the houses of the martyrs and greeted their families, but we couldn’t make it to the main road because the police was standing there,” she said.

With the internet cut off since the crackdown was launched 12 days ago, the protests have been organised by word of mouth and SMS messages. “I shouted to my neighbours telling them about the time of the protest, and in some cases people knocked on each other’s doors and called on them to come out,” another protester said.

There were also protests in the eastern city of Port Sudan.

Hafiz Ismail, an analyst with Justice Africa Sudan said the “demands of the street were clear”, but there has been no reaction to the protests from the Forces for the Declaration of Freedom and Change, a coalition of political groups that has represented the protesters in recent months.

A TMC spokesman earlier said an investigation had been launched into the attack on the protest camp earlier this week and that several military officers had been arrested over the “violations”.

Gen Shams Eddin Kabashi did not elaborate at a news conference late on Thursday beyond saying the alleged offences were “painful and outrageous”. He rejected all calls for an international investigation.

“We feel sorry for what happened,” said Kabashi. “We will show no leniency and we will hold accountable anyone, regardless of their rank, if proven to have committed violations.”

The exact death toll in the attack on the protest camp on 3 June is unclear because many bodies were dumped in the Nile in an attempt to hide the scale of the killing. Hundreds more were injured in widespread beatings and assaults. Doctors also told the Guardian paramilitaries may have carried out more than 70 rapes during the crackdown.

Stalled talks between the council and an alliance of opposition groups over who should control a transition towards elections collapsed after security forces attacked the sit-in protest .

There are fears that widespread violence in remote parts of Sudan is going unreported. The UN confirmed on Thursday that 17 people had been killed and more than 100 houses burned in Deleij village in Darfur earlier this week.

A man crouches inside a burned house in Deleij. Photograph: Reuters

Amnesty International said this week that it had new evidence showing that “Sudanese government forces, including the RSF and allied militias, have continued to commit war crimes and other serious human rights violations in Darfur”.

At least 45 villages had been completely or partially destroyed in the past year, Amnesty said. “In Darfur, as in Khartoum, we’ve witnessed the Rapid Support Forces’ despicable brutality against Sudanese civilians – the only difference being, in Darfur they have committed atrocities with impunity for years,” its secretary general, Kumi Naidoo, said.

The bloodshed in Sudan has prompted concern from some world powers, but the military council has been bolstered by support from Saudi Arabia and the United Arab Emirates, which between them have offered $3bn in aid.

The Ethiopian prime minister, Abiy Ahmed, visited Khartoum last week to mediate between military leaders and the opposition.

Trade sanctions were lifted in 2017, but Sudan is still on the US list of state sponsors of terrorism, which prevents it from accessing much-needed funding from international lenders. Washington has previously said it will not take Sudan off the list while the military remains in power.