It published the unusual allegations in an 8,000-word report on the incident after the Kremlin was accused of using a military grade nerve agent in Salisbury, on March 4.
Claiming that the substance used in the incident had been a nerve agent allegedly developed in Russia, London rushed to accuse Moscow of being involved in the case without presenting any evidence.
The report concluded: 'The situation around the Skripals looks more and more like a forcible detention or imprisonment'.
Mark Sedwill also said in a letter to NATO Secretary General Jens Stoltenberg that Russian Federation had previously tested whether door handles could be used to deliver nerve agents.
Last week, the chief executive of the Defense Science and Technology Laboratory in Porton Down, Britain's premier chemical weapons laboratory, said its scientists could not identify "the precise source" of the chemical, though its purity indicated that it was nearly certainly created by a "state actor".
"We didn't produce Novichok, we didn't store this Novichok, so-called under the Western classification, was never in our military forces".
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A program set up in Russian Federation in the 2000s trained personnel from special units in the use of chemical warfare agents, he said, including investigating how nerve agents could be administered through door handles.
Russian Foreign Minister Sergei Lavrov said on Friday a report by the Organization for the Prohibition of Chemical Weapons (OPCW) did not confirm the origin of the poison used against a former Russian spy, accusing his British counterpart of distorting the findings.
He also complained at the continued refusal of the British authorities to grant consular access to Ms Skripal following her discharge from hospital.
The letter adds that Russian intelligence services "view at least some of its defectors as legitimate targets for assassination".
United Kingdom officials have said Sergei Skripal, 66, and his 33-year-old daughter, Yulia, were poisoned when they came in contact with a chemical nerve agent at his home in Salisbury on March 4.
Mr Sedwill wrote: "We have information indicating Russian intelligence service interest in the Skripals, dating back at least as far as 2013, when email accounts belonging to Yulia Skripal were targeted by GRU [Russian military intelligence] cyber specialists". He said it was highly unlikely that any former Soviet republic besides Russian Federation pursued an offensive chemical weapons program. Sergei Kripal remains hospitalised, but British health officials say he is recovering.
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Russian Federation has charged that British officials are keeping Skripal's daughter in isolation.
Separately on Friday, Russia's ambassador to Britain said he was concerned the British government was trying to get rid of evidence related to the case.
Former KGB bodyguards identified as suspects in the murder denied any involvement.
"I want to underline: the OPCW only has confirmed the composition of the chemical agent", he said.
This is an image of the daughter of former Russian Spy Sergei Skripal, Yulia Skripal taken from Yulia Skipal's Facebook account on Tuesday March 6, 2018.
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