Egyptian authorities have forced a Guardian journalist to leave the country after she reported on a scientific study that said Egypt was likely to have many more coronavirus cases than have been officially confirmed.

Ruth Michaelson, who has lived in and reported from Egypt since 2014, was advised last week by western diplomats that the country’s security services wanted her to leave immediately after her press accreditation was revoked and she was asked to attend a meeting with authorities about her visa status.

On Sunday 15 March, Michaelson had reported on research by infectious disease specialists from the University of Toronto as well as public health data and news stories that pointed to Egypt having a higher rate of coronavirus cases than the number confirmed by the government.

She cited a study accepted for publication in the Lancet Infectious Diseases journal, which had analysed flight records, traveller data and infection rates to estimate that Egypt could have had 19,310 coronavirus cases by early March, with the lower end of the range about 6,000 cases. The Egyptian government’s official count at the time period covered by the data was that three people were infected.

The day after the story was published, Michaelson was called to a three-and-a-half hour meeting with officials including the chairman of the state information service (SIS), Diaa Rashwan, where she says she and another journalist who had tweeted about the research were accused of misreporting an unreliable study and spreading panic.

The Egyptian officials demanded the story be retracted or that the Guardian publish an official apology.

On 17 March, Michaelson’s press accreditation was revoked. The Guardian offered the Egyptian authorities the chance to write a letter for publication rebutting its report or the Canadian study, but received no response to the offer.

The following day, British diplomatic officials and the SIS passed on the message to Michaelson that she needed to meet Egypt’s visa issuance authority.

Michaelson, who is also a German citizen, said she was advised by German diplomatic officials in Cairo that she should not attend the meeting under any circumstances. “They said, ‘We do not believe it’s safe for you to go to this meeting. You’re at high risk of arrest and you should get on a plane,’” she said.

Flights out of Egypt were due to be suspended at noon the following day, Thursday, and with so many foreign tourists trying to flee the country as travel bans kicked in around the world, most planes were fully booked.

Michaelson said she was advised by the British embassy and her own contacts that members of the country’s security apparatus were seeking to immediately remove her from the country. “The national security agency told British diplomats that there was a plane one evening and they ‘wanted me on it’,” she said.

A lawyer who attended the meeting with the visa issuance authority on Michaelson’s behalf was given the same message, she added.

She left Egypt on a flight ferrying stranded tourists and foreign nationals to Germany on Friday evening.

Michaelson’s departure leaves the north African country with no full-time British newspaper correspondents. Bel Trew, a correspondent for the Times, was threatened with a military trial and expelled from Egypt in March 2018.

“The Guardian is a global news organisation that strives to report with clarity and integrity at all times,” a spokesperson for the Guardian said. “In this instance we reported on scientific findings by credible infectious disease experts. We have offered the Egyptian government opportunity to comment and respond to our reporting in the normal way.

“We regret that the Egyptian authorities have chosen to revoke accreditation from a reporter working for a trusted, independent media organisation like the Guardian.”

A spokesperson for the Foreign Office said: “The UK supports media freedom around the world. We have urged Egypt to guarantee freedom of expression. UK ministers have raised this case with the Egyptian authorities.”

Asked for comment, an Egyptian official directed the Guardian to a letter sent last week by the SIS to the newspaper’s editor-in-chief, Katharine Viner. It argued the University of Toronto research cited in Michaelson’s story relied on speculation, and that its approach and results had been rejected by the World Health Organization (WHO).

In fact, the WHO said it was unable to verify the methodology used in the study, and said its own data was drawn from hospitals, meaning there was often a reporting delay. “It is possible that there are many other cases with mild symptoms which did not result in hospital visits, and therefore are not detected or reported,” a WHO official told reporters in Cairo.

Egypt had 366 confirmed cases of the virus by Monday with 19 deaths, according to the country’s health ministry.

Press freedom in Egypt has severely deteriorated since the military took power in 2013 and the former commander-in-chief of the armed forces, Abdel Fatah al-Sisi, became president the following year.

The Committee to Protect Journalists said in its annual report last year that 26 reporters were detained in the country and that most had been prosecuted in groups on charges of terrorism and reporting false news.

Domestic media has gradually come to be dominated by the state, which exercises widespread censorship. The office of the country’s last major independent news outlet, Mada Masr, was raided late last year. Access to its website from inside Egypt has been blocked.