Vladimir Putin was likely to have known about the operation in London to murder the Russian dissident Alexander Litvinenko, Washington's top diplomat in Europe alleged in secret conversations in Paris.

Daniel Fried, the assistant secretary of state, questioned whether "rogue elements" in Russia's security services could have carried out the hit without Putin's direct approval.

A scenario where the Kremlin was unaware of the Litvinenko plot was far-fetched "given Putin's attention to detail", Fried said. The Russians were behaving with "increasing self-confidence to the point of arrogance", he told the French, arguing for a tougher stance towards Moscow.

Fried made his remarks just two weeks after Litvinenko died an agonising death from polonium-210 poisoning in a London hospital. On 7 December 2006 Fried met Maurice Gourdault-Montagne, senior diplomatic adviser to Jacques Chirac, France's president at the time.

Their talks in Paris took place against a backdrop of strained US-French relations following Chirac's criticism of the US-led invasion of Iraq, and just days after Litvinenko's dramatic death-bed statement. In it he directly accused Putin of poisoning him. The Kremlin rejects this.

Gourdault-Montagne adopted a "defensive posture" over Russia, a diplomatic cable records. "He showed reluctance to see the Kremlin's hand in the Litvinenko poisoning, preferring to ascribe it to rogue elements." He urged for the west to be careful in "managing the Russians".

Fried strongly disagreed: "Fried commented that the short-term trend inside Russia was negative, noting increasing indications that the UK investigation into the murder of Litvinenko could well point to some sort of Russian involvement.

"MGM (Gourdault-Montagne) wondered aloud who might have given the order, but speculated the murder probably involved a settling of accounts between services rather than occurring under direct order from the Kremlin.

"[But] Fried, noting Putin's attention to detail, questioned whether rogue security elements could operate, in the UK no less, without Putin's knowledge. Describing the current atmosphere as strange, he described the Russians as increasingly self-confident, to the point of arrogance."

The exchanges are likely to embarrass Gourdault-Montagne, France's ambassador in the UK since 2007. Fried, then US assistant secretary of state for European and Eurasian Affairs, is still a top US diplomat. Barack Obama has put him in charge of closing down Guantánamo Bay.

The leak will also displease the Kremlin and Downing Street. Both are anxious to improve bilateral ties and put the damaging Litvinenko scandal behind them. The British foreign secretary, William Hague, visited Moscow last month.

The cables released by WikiLeaks, however, provide further clues that suggest the Russians deliberately obstructed the Litvinenko investigation. A file from the US consulate in Hamburg reports how Dmitry Kovtun left "positive traces" of radioactive polonium-210 in Germany before departing for Britain.

Kovtun, a Russian businessman and ex-KGB agent, flew to Hamburg with Aeroflot on 28 October 2006. He flew on 1 November to London. Kovtun met Litvinenko later the same day in London's Millennium Hotel. Also at the meeting was Andrei Lugovoi, another ex-KGB officer accused by Scotland Yard of Litvinenko's murder.

Citing German detectives, the cable says Kovtun left a stunning radioactive trail of "polonium contamination" during his four-day stay in Germany. Kovtun deposited polonium in the Hamburg flat of his ex-wife Marina and in several other locations, including his former mother-in-law's house, the cable reports.

It cites Gerhard Schindler, Germany's deputy director general for counter-terrorism: "Schindler explained German officials retraced Kovtun's steps to and from his ex-wife's home in Hamburg. Schindler said Kovtun left polonium traces on everything he touched – vehicles, objects, clothes, and furniture.

"German investigators concluded Kovtun did not have polonium traces on his skin or clothes; Schindler said the polonium was coming out of his body, for example through his pores."

As part of their investigation German authorities tested the German Wings plane that Kovtun caught from Hamburg to London; they found no polonium. They then tried to test the Aeroflot plane that flew Kovtun to Germany "and had prepared to ground it upon its next arrival".

But the Russians were one step ahead: "Schindler said Russian authorities must have found out about German plans because 'at the last minute' Aeroflot swapped planes; Schindler said he did not expect Aeroflot to fly the other plane to Germany any time soon."

In November 2009, Germany – Russia's most important European partner – quietly dropped its case against Kovtun. Kovtun has said he has only one explanation: that he brought the contamination back from London after meeting Litvinenko in mid-October.

With the Kremlin offering protection to Lugovoi, US diplomats conclude in cables that the truth about the assassination is unlikely to emerge any time soon. Russia has refused to extradite Lugovoi, now a member of Russia's federal parliament, the Duma, with immunity from prosecution.

In May 2007 the US ambassador in Moscow, John Beyrle, reported that the Russians were "highly unlikely" to extradite Lugovoi to the UK despite the "long-term damage to Russia's reputation" caused by its refusal. Another cable by Beyrle's predecessor William Burns quotes the view of political analyst Stanislav Belkovsky that Lugovoi enjoys "the personal protection of Putin".

Elsewhere Burns trotted through the proliferating theories and conspiratorial accounts circulating in Moscow after Litvinenko's death. "The media have variously traced Litvinenko's demise to suicide, Putin's Kremlin, Putin himself, those determined to undermine Putin, FSB agents unhappy with Litvinenko's alleged betrayal of their organisation, those unhappy with Litvinenko's co-operation with Israel-based businessman [Leonid] Nevzlin on the Yukos affair, and the United States or 'other' countries." Much of this speculation was "self-serving", he said.

All theories were handicapped by a lack of evidence, Burns pointed out. Either way the affair reflected badly on Russia's leadership, since most reasonable observers were inclined to believe the worst of the Russian state. "Whatever the truth may ultimately be – and it may never be known – the tendency here to almost automatically assume that someone in or close to Putin's inner circle is the author of these deaths speaks volumes about expectations of Kremlin behaviour."