More than 1 million people in Africa have been infected by the Covid-19 virus, health authorities on the continent have announced.

Confirmed Covid cases in African countries have risen fivefold in the the past two months and more than doubled in July.

Reaching the landmark of 1 million cases will underline the spread of the pandemic in Africa, raising new concerns that frail healthcare systems will be overwhelmed as the infectious disease hits populations already weakened by poor diet or other illnesses.

According to the the African Union’s Centres for Disease Control and Prevention (CDC), more than 700,000 have recovered from the disease so far, and 22,000 have died.

There are widespread concerns that official figures represent only a fraction of the casualties of Covid-19 on the continent.

Some experts describe the official totals compiled by the World Health Organisation from statistics supplied by governments as “the the tip of the iceberg” and say the true total is 10 or even 100 times higher.

Low testing, a lack of political will, prejudice against victims, poor infrastructure and communications are among the many factors that obscure the true picture of the pandemic’s impact on African countries, the experts told the Guardian.

Some countries on the continent – such as Tanzania – have failed to provide any useful statistics to the World Health Organization for months, while others have reported counts so low they stretch credibility.

“The continent is at a pivotal point,” said Dr Matshidiso Moeti, WHO Regional Director for Africa, last week. “The virus has spilled out of major cities and spread into distant hinterlands. Countries need to keep apace and urgently decentralise their key response services. We can still stop Covid-19 from reaching full momentum, but the time to act is now.”

In May, the WHO raised the possibility that the disease could “smoulder” in Africa for many years to come after killing as many as 190,000 people in the 12 months. The organisation predicted between 29 million to 44 million people could become infected in the first year of the pandemic if containment measures fail. This “would overwhelm the available medical capacity in much of Africa” where there are only nine intensive care unit beds per million people.

South Africa, Algeria, Egypt, Ghana and Nigeria currently account for about 75% of the cumulative Covid-19 cases in Africa. Everywhere, the youth of populations relative to Europe has helped keep mortality rates low.

Zweli Mkhize, South Africa’s health minister, gave an upbeat assessment on Wednesday, saying that some evidence suggested the peak of infections in the most populous and connected parts of the continent’s most industrialised country had passed.

“We have not breached our bed capacity and many of our field hospitals are not filled to capacity and we continue to monitor this as we manage the surge … The real risk of experiencing the ‘second wave’ of the pandemic remains, so containment measures must never be abandoned,” Mkhize said.

Scientists in South Africa, where statistics are seen as broadly reliable, recently estimated more than 28,000 excess deaths have been recorded since early May, suggesting that the true number of fatalities caused by the pandemic is several times higher than the government count of just over 7,000 confirmed Covid-19 deaths.

Mkhize said new efforts would be made to collect information on “sudden deaths and deaths that occur at home”.

One problem across the continent is a long-term failure to register deaths. Only eight countries in Africa record more than three out of every four of deaths, according to the United Nations.

“It is astounding that in the 21st century we still don’t know how many people are born, die and what they die from in countries where such data is sorely needed to guide vital healthcare strategies,” said Dr Philip Setel, vice president for civil registration and vital statistics at the global health organisation Vital Strategies.

“In South Africa there is good mortality data, but in most sub-Saharan countries I don’t think we do understand the full picture of the pandemic.”

Widespread stigma against Covid victims is also a problem. The way people were treated early in this pandemic is “just like the way, early on in the HIV epidemic, patients were being treated,” Salim Abdool Karim, an epidemiologist who chairs South Africa’s COVID-19 ministerial advisory committee, told a World Health Organization event last month.

Now, some people avoid testing for the coronavirus “because if they test, they’re ostracised,” Karim said.

In Somalia, “our teams are seeing people who have tested positive running away from their homes out of fear of being stigmatised by the community,” Abdinur Elmi, an official with the aid group CARE, said in a statement.

Last week the International Rescue Committee (IRC), said the lack of reliable data left the effort to counter the disease “in the dark”. Though the WHO recommends at least one test per 1,000 people per week, countries like Niger and South Sudan have not managed more than one test per thousand in the five months since the outbreak began.

Resources remain scarce, with limited supply of key materials and a lack of funding for many testing programmes across the continent.

“Much more is going on than meets the eye,” said Michelle Gayer, director of emergency health at the IRC. “We really need to ramp up testing. Without knowing the extent, you are not taking appropriate action. The financial part is really important. The UK and the US have done millions of tests, and we need that kind of capacity [in Africa].”

Researchers have been forced to seek new ways of monitoring the spread of the disease, such as observing the rate at which graves are dug or counting Google searches for information on Covid-19 symptoms.

In Ethiopia, where fewer than one in 50 deaths are officially registered, a scheme set up to monitor deaths related to HIV/Aids a decade ago has been repurposed to focus on the new threat. Elsewhere, nations are restarting programs set up during Ebola outbreaks.

In Nigeria, media reports citing gravediggers alerted authorities to an undetected Covid-19 outbreak in the northern city of Kano in April, when deaths surged from a daily average of 11 to 43. In Somalia, the mayor of Mogadishu admitted dramatically higher death tolls after an investigation by the Guardian.

Last week the WHO said that nine countries in sub-Saharan Africa were reporting a decline in cases.

Many countries in Africa imposed strict lockdowns which inflicted significant hardship on hundreds of millions of people across the continent living in crowded and often unsanitary conditions. Many depend on earnings during the day to be able to eat and there are widespread reports of hunger.

A range of innovative solutions are being considered to the lack of hard data. Surveys conducted by mobile phone could be another way to measure deaths.

“To complement rapid mortality surveillance, mobile phone surveys are a potential innovation that might be a quick way to obtain a snapshot of the mortality at a national level,” said Setel. “Though this method still needs validation, is it one worth exploring.”