The European court of human rights has accused British newspapers, including the Daily Mail, of publishing "seriously misleading" reports.

A statement issued by the registrar of the court and emailed to reporters last Friday, says the court is "concerned about the frequent misrepresentation of its activities in the British media". The registrar, Erik Fribergh, is the court's senior staff lawyer.

This is thought to be the first time the registrar has responded formally to media reports, although the court did test the ground with a more low-key response a week earlier.

That came in the form of an email from the court's press service on 4 October telling journalists a report in the Mail a day earlier had been a "serious misrepresentation" of comments by the court's UK judge.

The newspaper alleged that the judge, Paul Mahoney, had "called for axe-murderers to be given the vote". In fact, said the court, Mahoney had said it was important for the UK to implement the Hirst judgment of 2005, which decided that the blanket ban on voting by convicted prisoners was unlawful.

John Hirst, who brought the case, admitted manslaughter in 1980 after battering his landlady to death with an axe. Last week, the Daily Mail reported that judges at the human rights court had handed 202 criminals "taxpayer-funded payouts of £4.4m – an average of £22,000 a head". Its report was followed up by the Daily Telegraph and other papers.

The story came from a written Commons answer to Philip Davies MP on 10 September. Davies had asked the Ministry of Justice about "damages, costs or compensation" awarded by the human rights court since 1998. The government's 30-page response was published by the Commons library.

That document, based on published information, clearly distinguishes between costs – which the losing government has to pay to a successful applicant's lawyers – and damages, which are intended to compensate the person whose rights have been breached by the government's failure to comply with the human rights convention.

According to the registrar's statement, the total paid in compensation since 1998 is in the region of £1.7m, far less than half the figure calculated by the Daily Mail. Since the court rarely pays lawyers all the costs they have claimed, it is likely that the total sum kept by successful applicants after settling their lawyers' bills is even lower.

"The failure to distinguish between compensation and costs creates the impression that applicants were awarded significantly more compensation than they really were and that the sums indicated were for the applicants' sole benefit," Fribergh says.

"For example, one of the articles suggested that Mustafa Abdi 'pocketed £7,237', whereas in reality he was awarded €1,500 [£1,280] in compensation. It is also indicated that applicant Douglas Vinter was 'awarded £34,500', although he was accorded no compensation whatsoever, the sum cited relating solely to costs and expenses."

Explaining why costs normally exceed compensation in UK cases, the registrar says that legal fees are particularly high in the UK. He points out, for example, that a successful challenge by the Guardian and four other news groups over the protection of their sources led to a total award in 2009 of £143,000 in legal costs – but no compensation at all. The news groups had claimed reimbursement of nearly £767,000.

Nor was it true to say that damages were invariably paid to criminals. Among successful claimants were joiners who had been blacklisted because they were Catholics, a boy who was assaulted by his stepfather and the family of a man murdered by a stalker.

The registrar also points out that the 202 cases lost by the UK in 15 years, described by the Mail as staggering, amount to 1.5% of the 13,515 UK cases considered by the court.

After a weary denial of newspaper claims that Strasbourg judges are "unelected" and "not even legal experts", Friberg says the court is "concerned about the frequent misrepresentation of its activities in the British media, the confusion between the costs (awarded in all properly functioning judicial systems) and compensation being one example of how a distorted picture of the court's decisions and work has been put forward."

What the Strasbourg judges apparently find hard to understand is why reporters might fail to check their conclusions with the court's press office or seek a response from the court. Although many courts publish press summaries of their decisions, it is unprecedented for any court to respond to what it regards as inaccurate reporting of its work in the UK.

Ironically, the court's response to the media seems to have come at the moment when senior journalists are talking about bringing a human rights challenge to the government's plans for press regulation.

The court's patience seems finally to have snapped after years of regarding itself as powerless to prevent misreporting. What seems to have brought this about is far from clear. It is not likely to have been Ed Miliband's recent spat with the Daily Mail, although that might have emboldened other critics to take the newspaper on.

Perhaps the court thinks that a climate of misrepresentation provides a fertile soil for Conservative politicians, such as the justice secretary and the home secretary, who argue that the UK should no longer be bound by its decisions. Strasbourg is not prepared to go down without a fight.