The rule of law in Europe is facing its most serious crisis since the end of the cold war, according to the chief executive of Europe's largest human rights body.

Thorbjørn Jagland, secretary general of the 47-nation Council of Europe, made his assessment before tensions in eastern Ukraine rose over the weekend and before the council's parliamentary assembly voted last Thursday to suspend Russia's voting rights over its annexation of Crimea. Jagland argues that a lack of human rights in Ukraine has paved the way for Russia's actions.

He writes: "In Ukraine the absence of an independent judiciary, and lack of the checks and balances which a functioning parliament and free media should provide, allowed endemic corruption and misuse of power to thrive unchecked. This caused mistrust, social unrest and ultimately a revolution."

Jagland addressed his remarks to member states in an unpublished report on the state of democracy in Europe. The report is due to be released after it has been considered by delegations from the member governments meeting at a summit in Vienna early next month.

Most of the 72-page report is devoted to identifying "very worrying" challenges to human rights, democracies and the rule of law across Europe.

These include discrimination against ethnic and national minorities (in 39 member states); prison overcrowding (30 states); corruption (26 states); ill treatment by police (23 states); social exclusion and discrimination against Roma (20 states); and restrictions of free expression (eight states).

Problems with the judiciary are identified in 20 countries and deeply embedded judicial corruption has been reported in "many" of the 47 Council of Europe states, the report says. In some, the justice system was "completely corrupt". The European court of human rights, which is operated by the Council of Europe, continues to find violations of the right to a trial within a reasonable period of time. In some states, prosecutors sit in court alongside the judges, exercising powers that are too broad and lack transparency.

To avoid the risk that its publication will be vetoed by member states, the report does not name and shame individual governments. But each country was told last November, in confidence, of the three main challenges it is seen as facing. These are not necessarily its worst violations of human rights; they may include persistent and politically difficult issues as well as those that the Council of Europe believes it can best assist in overcoming.

These problems are not confined to eastern Europe. Calling for an improved gender balance within the judiciary, the report notes that two countries have supreme courts that are over 90% male. The UK must be one of them.

"Senior members of the executive branch in some member states have publicly criticised court decisions," the report continues. That was certainly a problem in the UK at one time, although it is fair to say that members of the present government have been more restrained.

More broadly, the council's monitoring bodies have raised concerns about police and prisons as often in northern and western Europe as in central and eastern Europe. Discrimination and social exclusion are widespread, although targeted groups vary from region to region.

The report identifies more effective monitoring as one of the paths to progress. Some standards, such as freedom of expression, are not specifically monitored within Europe. Others, such as the status of minorities, are monitored by overlapping bodies. And some bodies are too slow to cope with emergencies. The report also finds that some countries are reluctant to seek help because of the damage to the state's reputation that might follow.

It offers reassurance that Europe is not divided into countries that have human rights problems and those that do not. But it adds that Europe can be divided into those that are willing to co-operate in addressing their problems and those that are unwilling to do so.

Inevitably, increased monitoring and support will cost more money, which would have to come from member states – although Jagland says that reforms in recent years have led to a "leaner and more efficient organisation". He also wants to hold a summit next year at which heads of state would agree a five-year agenda for democratic security.

If this goes ahead, its recommendations are bound to need funding. But if they give member states less justification for invading each other's territory, it would surely be a small price to pay.