Kremlin spokesman Dmitry Peskov said the eminent academics, Anatoly Maslov, Alexander Shiplyuk and Valery Zvegintsev, all face ‘very serious accusations’.

The trio have all worked on the weapons for years and were among the authors of a book chapter entitled ‘Hypersonic Short-Duration Facilities for Aerodynamic Research at ITAM, Russia’.

Putin has long boasted that Russia is the global leader in hypersonic missiles and unveiled his ‘Kinzhal’ rockets in 2018, hailing them as ‘undefeatable’ by any present or future defence systems.

But he faced fresh humiliation on Tuesday when Ukraine said it had destroyed six of them in a single night.

The arrests have spread alarm through Russia’s scientific community.

Colleagues of the three men published an open letter protesting their innocence and warning the prosecutions posed serious risk to Russian science.

‘We know each of them as a patriot and a decent person who is not capable of doing what the investigating authorities suspect them of,’ they said.

‘In this situation, we are not only afraid for the fate of our colleagues. We just do not understand how to continue to do our job.’

The letter cited the case of Dmitry Kolker, a Siberian scientist who was arrested last year on suspicion of state treason and flown to Moscow despite suffering from advanced pancreatic cancer.

The laser specialist died two days later. It said such cases were having a chilling effect on young Russian scientists.

‘Even now, the best students refuse to come to work with us, and our best young employees are leaving science,’ the letter stated.

‘A number of research areas that are critically important to laying the fundamental groundwork for the aerospace technology of the future are simply closing because employees are afraid to engage in such research.’

Kremlin spokesman Dmitry Peskov said the eminent academics all face ‘very serious accusations’

Asked about the letter, Peskov said: ‘We have indeed seen this appeal, but Russian special services are working on this. They are doing their job. These are very serious accusations.’

Ukrainian air force spokesman Yurii Ihnat said the country’s air defences, bolstered by Western-supplied systems, had thwarted an intense Russian attack.

He said the barrage included six Kinzhal aero-ballistic hypersonic missiles, the most fired in a single attack in the war so far. All were shot down, he added.

Putin has repeatedly touted the Kinzhals as providing a key strategic competitive advantage and among the most advanced weapons in his country’s arsenal.

The missiles are difficult to detect and intercept because of their hypersonic speed and manoeuvrability.

If Ukraine’s claim of having shot down six fired Tuesday is confirmed, it would mark another blow to Putin’s war efforts and show the increasing effectiveness of the country’s air defences.

Russian Defense Minister Sergei Shoigu contested the Ukrainian claims, telling the state-run RIA-Novosti news agency: ‘We have not launched as many Kinzhals as they allegedly shoot down every time with their statements.’