The Mozambican government failed to warn people in the areas worst hit by Cyclone Idai despite a “red alert” being issued two days before it struck, the mayor of the city of Beira has said.

The southern African country was completely unprepared for the disaster and “profound negligence” led to many deaths, said the mayor, Daviz Simango, who is also the leader of an opposition party.

More than 460 Mozambicans died in the disaster, according to official numbers, though the final figure is expected to be far higher when flood levels recede and their bodies can be found. The effects are still unfolding: about 3 million people across Mozambique, Malawi and Zimbabwe, more than half of them children, urgently need humanitarian help, Unicef said on Wednesday.

Simango said that although his city was 80% destroyed, only about 20 people from Beira died, while in communities outside Beira the death toll was “scary”. This was because when a red alert was issued two days before Cyclone Idai struck, city authorities made sure people knew it was coming, but the same did not happen in rural areas, he said.

“This indicates that the central alarm system did not work – people were not warned in the areas at risk,” Simango said. “There was no mapping of areas vulnerable to flooding. I have the impression that the authorities did not do their homework, and there was profound negligence in how the red alert was managed.

“Mozambique was not prepared. There were no boats, there were no helicopters, no means of saving lives. Most of the people saved were rescued by help coming from outside. The internal capacity to respond immediately to disasters like this is zero, and the result is that with every new day, the list of the dead is updated.”

It was the South African air force and the Indian army, which happened to have a ship in the area, that drove the rescue effort initially.

Now, while more than 130,000 newly homeless people have been taken into reception centres, flood levels are very slowly receding in some areas. More flooding could be on the way: the Mozambican president said that he is worried about the structural integrity of dams including Cahora Bassa, the fourth largest in Africa, and that water may have to be released as the rains are not letting up.

“They launched the red alert, but I doubt they even know what a red alert means,” said Adriano Nuvanga, the former head of the country’s public integrity centre, adding that he saw a “great corrosion of the state’s ability due to corruption”.

Five cases of cholera have been reported, and the “total lack of preparation and resources” to deal with the cyclone may extend to an inability to cope with the outbreaks of disease that often follow natural disasters, according to Henriques Viola, the secretary general of the medical association of Mozambique.

“Epidemics of malaria, diarrhoea and cholera are on their way, and I don’t know to what extent we’re ready to deal with them,” Viola said, adding that it was a scandal that the rescue and aid efforts were being largely carried out by the international community because Mozambique lacked the “institutional capacity”.

“The government should have taken more action than it did. The response, though it existed, was not what we expected,” he added. “The state is responsible for the protection of its citizens and I think we have to think about this issue.”

The legacy of hundreds of years of colonialism and a 15-year civil war has left Mozambique extremely poor, unable to provide basic services for its people and withstand the shock of recurrent floods. The discovery of natural gas in 2011 raised hopes that increased revenues would transform the country, but it has since become mired in a secret debt scandal that pushed it into financial crisis.

The government took out $2bn of secret debt, organised at the London offices of the Russian state-owned bank VTB and Credit Suisse. An audit by the corporate investigation firm Kroll could not account for a quarter of the money; an indictment was filed in a US court and three former Credit Suisse bankers and Mozambique’s former finance minister have been arrested.

Donors, who stopped vital budget support when details of the scandal emerged, are expected to be wary of supporting the huge reconstruction effort that will be needed unless they are assured that their money will not be stolen.

Simango said the government was mobilising massive support in Beira’s name, and called for an audit of all the donations pouring in to ensure that it reached the people it was intended for. “If we want credibility and for the country to be respected, there must be an audit,” he said.