The Russian state directed and ran the military coup in Crimea and its subsequent annexation in 2014, Ukraine has told the European court of human rights.

The case in Strasbourg is one of a series brought by the Ukrainian government designed to expose alleged Russian state complicity in human rights abuses. It has the potential to embarrass Vladimir Putin and lead to Ukrainian demands for reparations from Russia.

Russia rejects allegations it was responsible for the annexation and sought on Wednesday to strike out the case in an attempt to stop it proceeding to its next stage – gathering of direct evidence.

Ben Emmerson QC, representing the Ukrainian government, told the court Ukraine lost control of Crimea on the day of the coup not as a result of unilateral action by armed separatists but “as the result of a military invasion by the armed forces of the Russian Federation, aided and abetted by pro-Russian political and paramilitary proxies in Crimea”.

Russia warned Europe’s human rights tribunal it risks opening a “Pandora’s Box” of politically motivated cases if it accepts Ukraine’s claims that Moscow-led forces committed atrocities in the Crimea.

The case comes at a politically sensitive time, as the new Ukrainian president, Volodymyr Zelenskiy, explores the possibility of fresh talks with Putin over the future of both the occupied Donbass region and Crimea. An unprecedented prisoner swap at the weekend opened the door to a new climate but the pursuit of the ECHR case shows how determined Ukraine remains to force Russia out of its country, including Crimea.

Emmerson insisted Russia was legally answerable for human rights violations – not as the territorial sovereign – but as an occupying power. He said claims that Crimea transferred its sovereignty to Russia was based on a “transparent legal fiction” and a bogus referendum in which the option of the status quo was not offered.

To accept “Russia’s claim to sovereignty over Crimea would undermine a critical cornerstone of international law – the prohibition on the use of force by one nation on the sovereign territory of another without its consent, without a resolution of the United Nations security council, and in the absence of any possible claim to self-defence.”

Citing evidence compiled by the UN’s high commissioner for human rights, Emmerson said: “Once the occupation was fully established, a sustained campaign of political repression then began.”

Painting what he describes as a dystopian picture of Russia’s authoritarian grip on power, he said: “Russian citizenship was imposed on all residents of Crimea. Non-Russian media outlets, including Ukrainian and Tartar television channels, were closed down. Peaceful protests against the Russian occupation were banned. Vast swathes of private property were unlawfully appropriated without compensation.”

In just one day, Russia had occupied Crimea militarily and assumed effective overall control of the territory. It had successfully installed a subordinate local administration that was entirely dependent upon Moscow for its military, economic and political survival.

He said particular intimidation was occurring at the military commissariat in Simferopol, a camp guarded by Russian soldiers.

He also condemned the Russian tolerance of, and blanket amnesty given by Russia to Crimean paramilitary forces. “The chilling message is that resistance to the occupation is not only futile but also extremely dangerous – because the rule of law will be applied selectively. Those who support the Russian regime are free to commit criminal acts against those who oppose it, safe in the knowledge that their crimes will almost certainly go unpunished.”

Crimea, he said, “has become an accountability wasteland for those seeking accountability for those opposing the Russian state occupation. That is no accident. It is evidence of a tacit policy.”

Separate cases are being taken to the ECHR by the Ukrainian government over the Russian occupation of the Donbass region in eastern Ukraine and the shooting down in 2014 of the Malaysia Airlines flight MH17 over Ukraine that killed all 283 passengers onboard.