One of Japan's leading newspapers has been forced into a climbdown over serious errors in articles about two of the most contentious issues in the country: the Fukushima nuclear disaster and the use of wartime sex slaves.

Executives at the Asahi Shimbun, a left-leaning daily whose morning edition has a circulation of 7.6m, said the newspaper's executive editor, Nobuyuki Sugiura, would be dismissed and other staff severely punished.

The newspaper retracted a 20 May article in which it claimed that about 650 Tepco workers at Fukushima Daiichi, 90% of staff, had defied an order by the plant's then manager, Masao Yoshida, to stay and make a last-ditch effort to regain control of the reactors in the days after the earthquake and tsunami hit in 2011.

The article, citing leaked testimony from Yoshida, claimed that the workers fled to the nearby Fukushima Daini nuclear facility three days into the crisis, as the pressure and temperature inside one of the damaged reactors reached dangerous levels.

But Yoshida's testimony before the government panel, which was released this week, contradicts the paper's claim. He said that although he had not asked workers to evacuate to Fukushima Daini, he thought it had been "perfectly reasonable" for them to go to the site, 6 miles (10km) away.

The Asahi's president, Tadakazu Kimura, told a packed press conference that an internal investigation had found the article to be incorrect. "We have caused significant damage to the trust our readers place in us," he said.

Kimura, who said he would decide on his own future at the paper at a later date, attributed the error to the reporters' "mistaken assumptions and insufficient checking. I offer profound apologies to our readers and people at Tokyo Electric Power."

Yoshida died of throat cancer last year, aged 58. Doctors said his illness had not been caused by exposure to radiation.

In his testimony, given over several months from July 2011 and running to 400 pages, Yoshida said that although non-essential workers were encouraged to go home, he and other Tepco officials at the plant had always intended to retain a skeleton staff to tackle the crisis.

That version appeared to be challenged in testimony given by the government's spokesman at the time, Yukio Edano, who told the same panel that Tepco's then president, Masataka Shimizu, had called him and mentioned a possible withdrawal. "I don't clearly remember [his] exact words … but I'm sure it was about a complete withdrawal," Edano said, according to a translation by Kyodo.

Yoshida was scathing about senior Tepco executives and politicians, whom he accused of failing to grasp the gravity of the situation and of causing confusion.

The Asahi's claims about fleeing Tepco workers were repeated by the international media. Other Japanese newspapers claimed their interpretation of Yoshida's leaked comments on the evacuation differed significantly from those of the Asahi.

The Asahi recently admitted that articles it ran in the 1980s and 90s on the diplomatically explosive subject of Japan's use of sex slaves before and during the second world war were also false.

The articles were based on the testimony of Seiji Yoshida, a former soldier who claimed he had witnessed women from the South Korean island of Jeju being abducted to work as sex slaves in military brothels.

Seiji Yoshida, who died in 2000, has been discredited by independent investigations by academics and other newspapers.

Despite issuing a retraction earlier this summer, the Asahi came under pressure to issue a public apology.

"I apologise to readers for publishing the erroneous articles and being too late in making the correction," Kimura said on Friday.

While Seiji Yoshida's false testimony does not in itself disprove the existence of tens of thousands of mainly Korean wartime sex slaves, the Asahi's errors have encouraged historical revisionists who insist the women were not forced to work in frontline brothels.

The prime minister, Shinzo Abe, who has voiced doubts that the women were coerced, said erroneous reporting of the issue had "caused agony to many people and damaged Japan's international reputation".

Speaking on a radio programme, Abe added: "Generally speaking, media reports have significant influence inside and outside the country and sometimes dishonour our country."