For more than three-quarters of a century, the story of Lidice has stood as haunting testimony of Czech suffering and victimhood at the hands of cruel Nazi occupiers.

The village, 16 miles from Prague, was razed to the ground, its adult male population murdered and its women and children transported to concentration camps – where the majority died – after Adolf Hitler singled it out in retribution for the assassination in 1942 of Reinhard Heydrich, deputy leader of the SS, by British-trained Czech and Slovak resistance fighters.

Now a political row has erupted over the atrocity after information emerged that a Jewish woman who had been secretly living there during the war was arrested – allegedly after being denounced by a neighbour – shortly before it was targeted for reprisal. She died in the Holocaust.

The disclosure, by a Czech historian, Vojtěch Kyncl, has cast a shadow over the village’s status as symbol of national martyrdom – a status cultivated first by the communist regime that ran Czechoslovakia until the 1989 “Velvet Revolution” and then by its democratic successors.

At the government’s insistence, it has led to the departure of Martina Lehmannová, director of the Lidice memorial – a museum, plaques and statues on the site of the original village.

At stake, some observers say, is the right to interpret the country’s 20th-century history freely: critics fear politicised attempts to censor second world war events comparable with recent alleged interference in neighbouring Poland and Hungary.

“I think academic freedom is in danger,” said Muriel Blaive, a historian of communist-era eastern Europe. “If they can intervene and fire someone just like that, it’s not a good sign. The temptation is clearly there to try to control the interpretation of history, as in communist times. The communists used to say: ‘Whoever controls history controls the present.’”

Štěpánka Mikešová, 35, had converted to Christianity to avoid detection and was living with a local family when she was detained by Czech police two days before Heydrich died of hiswounds on 4 June 1942. She was handed to the Gestapo and transported to Auschwitz, where she died the following August.

Details of her arrest were discovered in a chronicle written shortly after the war by the arresting police officer, Evžen Ressl, who said she was detained because her Jewish origins had been brought to the authorities’ attention by a Lidice resident. Some have questioned the truth of his account, suggesting he may have invented the story of Mikešová having been denounced.

Facebook Twitter Pinterest Schutzpolizei Nazi police pose among the ruins of Lidice. Photograph: Keystone-France/Gamma-Keystone via Getty Images

The revelations have provoked a backlash from survivors, including Marie Šupíková, daughter of the woman said to have denounced Mikešová. Šupíková, 87, who was handed to a German family after Lidice’s destruction and testified as a child witness at the postwar Nuremburg war crimes tribunal, rejects suggestions her mother, Alžběta Doležalová – who died in 1946 of tuberculosis contracted as an inmate at Ravensbrück concentration camp – was guilty of denunciation.

Lehmannová was ousted as memorial director after Šupíková and seven other survivors – under the auspices of the Czech Union of Freedom Fighters, a local group with roots in the former communist regime – wrote to senior politicians, complaining she had failed to contradict Kyncl’s research in a TV documentary aired last June on the anniversary of Lidice’s annihilation.

Instead, Lehmannová had told the programme that she would consider honouring Mikešová at the memorial.

The complaint prompted the intervention of Lubomír Zaorálek, the Czech culture minister, who accused the director of failing to empathise with the survivors and told her to resign or face being sacked.

Lehmannová – who chose to resign, prompting 10 other board members to quit in support – remains unapologetic. “The criticism was that I didn’t say that this [the arrest of Mikešová] never happened,” she told the Observer. “They know the story is true, but the problem is that the narrative of Lidice is no longer as crystal clear as they want. It spoils the pure-victim status.

“There are many stories from the second world war that describe very complicated things. But we are now in the 21st century and we cannot pick and choose information from the past. We cannot say this or that story is inconvenient to what we previously knew.”

She has been replaced by Eduard Stehlík, a military historian and ex-army officer who has written two books on Lidice. He has cast doubt on Kyncl’s research and declared that Lidice has been “pilloried”.

Kyncl, a member of the Czech academy of sciences, has insisted his account of Mikešová’s arrest is accurate and voiced support for Lehmannová. “I have the original official documents that were approved and verified by his [Ressl’s] gendarmerie superiors,” he said. “I have no doubt as to [their] authenticity.

“Martina Lehmannová only fulfilled her duty. The political affair was used to return the interpretation of history in the spirit of the former communist regime,” he said.

• This article was amended on 16 March 2020 because an earlier version incorrectly referred to Heydrich dying from “gunshot wounds”.