"Russia is acting against the U.K.'s national interest in cyberspace", Martin wrote in the letter.
"The risk that the Russian government, whether acting on its own or in collaboration with Kaspersky, could capitalize on access provided by Kaspersky products to compromise federal information and information systems directly implicates US national security".
Following her warning, Ciaran Martin, chief executive of the NCSC, said Russian Federation had targeted British infrastructure, including power and telecoms.
Two months ago, U.S. officials ordered federal agencies to remove the company's products from their networks after Russian hackers were reportedly found using Kaspersky.
The NCSC is understood to have been in dialogue with Kaspersky Labs and says it will explore ways of mitigating the risks to see if a system can be developed to independently verify the security of its products.
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Kaspersky's spokesperson called allegations of ties to the Kremlin "completely unfounded" at the time, and said that Russian laws and policies are being "misinterpreted".
Around the world, 400 million people use Kaspersky products.
Kaspersky Lab said in a statement that it looked forward to working with the NCSC on the issue.
The agency's technical director, Ian Levy, said he saw "no compelling case at present to extend that advice to wider public sector, more general enterprises, or individuals".
The guidance stated that its decision "will also apply to some Official tier systems as well, for a small number of departments which deal extensively with national security and related matters of foreign policy, global negotiations, defence and other sensitive information".
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"Whatever you do, don't panic".
Eugene Kaspersky, the CEO of the company, told Sky News in October his company had a "strong relationship" with Russian cyber police but they never engaged in espionage activities.
He denied claims the Russian state could use the company. "There are no facts about that", he added.
US authorities are investigating alleged Russian meddling in the 2016 presidential election, and some British lawmakers have called for a similar probe into the U.K.'s European Union membership referendum.
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