The Skripals survived the attack but a British woman died in June after her partner picked up a discarded perfume bottle that investigators believe contained Novichok.
Igor Korobov, 62, who headed the defence ministry's Main Intelligence Directorate (GRU) since 2016 and was the target of US sanctions, died on Wednesday after a 'long and serious illness'.
The GRU has also recently faced accusations that it carried out large-scale cyber attacks including a foiled attempt to hack into the computer system of the global chemicals watchdog.
Yakovenko claimed Moscow was the victim of an aggressive anti-Russian campaign by the British government,
Intelligence experts say the GRU has stepped up its activities including black operations - covert missions that are not attributable to the organisation carrying it out - as tensions mount between Russia and the West.
The US indictments were announced as Dutch security services thwarted a Russian attack on global chemical weapons watchdog OPCW, and after Britain blamed the GRU for plots that targeting the US Democratic Party and world sport's anti-doping authority.
Researchers at the Royal United Services Institute (RUSI) in London said Russia often conducts cyber attacks to simply show it is capable of disrupting the networks of a potential enemy.
The Netherlands expelled four alleged Russian agents in April after uncovering a spy-novel-style bid by Russia's GRU military intelligence agency to target the Organisation for Prohibition of Chemical Weapons (OPCW) in The Hague.
The US ambassador to London, Woody Johnson, and the Australian government have offered their support for Britain's stance against Russia.
Perdana Menteri Theresa May menyalahkan kerajaan Rusia dan menggambarkan suspek sebagai pegawai perisikan GRU.