Marina Litvinenko said her former KGB agent husband had written an article shortly before his death in November 2006 that questioned why Mr Putin had kissed a young boy’s stomach under his T-shirt during a tour of the Kremlin.
The inquiry, at the Royal Courts of Justice in London, was shown a copy of the article featuring a photograph of Mr Putin and the boy, with the headline “Kremlin Paedophile”.
Giving evidence yesterday, Mrs Litvinenko, 52, said: “It was written in 2006 after everybody saw how Putin behaved when he met a little boy in a Kremlin tour group. He went under his T-shirt and kissed his stomach.”
Robin Tam, QC, counsel to the inquiry, asked: “You have no idea if that allegation is true?” She replied: “No, I have no idea.”
She told the inquiry her husband had been paid £2,000 a month for “consulting” for UK intelligence services after claiming political asylum in the UK.
Mr Litvinenko, 43, died at University College Hospital in London nearly three weeks after drinking tea laced with radioactive polonium-210 as he met two Russian men – one a former KGB officer – at the Millennium Hotel in London’s Grosvenor Square.
His family believes he was working for MI6 at the time and was killed on the orders of the Kremlin.
Former KGB bodyguard Andrei Lugovoi and Dmitri Kovtun have been identified as the prime suspects in the killing.
Mrs Litvinenko denied her husband had been “employed” as an MI6 agent but said he did “consult” British and Spanish intelligence services after fleeing Russia.
Asked by Mr Tam whether Mr Litvinenko had provided the names of Russian sleeper agents to MI6, she replied: “I have no idea.”
Mrs Litvinenko said her husband had written books about Mr Putin and corruption within the Federal Security Service (FSB), the KGB’s successor.
She said Mr Litvinenko had claimed the Russian president was a KGB informant during his university years, that he had links to criminal gangs while serving as deputy mayor of St Petersburg and that he had penetrated the circle of advisers to the country’s former leader Boris Yeltsin.
His “most famous allegation”, however, was his claim that the FSB planned the Russian apartment bombings in 1999, which claimed 293 lives and led to the second Chechen war, Mrs Litvinenko added.
She also said the family’s phone had been bugged after her husband gave a televised press conference in Russia in 1998 in which he claimed he had been asked by senior FSB officers to kill the billionaire Boris Berezovsky.
The inquiry heard Mr Litvinenko feared for his life when he gave a press conference later that year in which he discussed the alleged plot.
The inquiry continues.