Acting Secretary of Homeland Security Elaine Duke ordered all government offices to remove and replace any of the company's popular anti-hacker software in use within 90 days.
"The department is concerned about the ties between certain Kaspersky officials and Russian intelligence and other government agencies," Duke said in a statement.
She also expressed concern that Russian intelligence agencies can by law request or compel assistance from Kaspersky, including in intercepting communications transiting Russian networks.
The move comes amid heightened strains between Russia and the US over Moscow's alleged interference in last year's US presidential election.
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Kaspersky was already finding the government shut to its business, according to US companies it competes with.
Earlier this year six top intelligence and security officials told a Congressional hearing that they would not use Kaspersky software.
In July the government's General Services Administration issued an advisory against using it.
Based in Moscow, Kaspersky has been selling its popular and highly regarded software around the world for two decade and does 85 percent of its business outside of Russia, including with multiple governments, according to the company.
It has repeatedly denied having anything more than business ties to the Kremlin.
"Kaspersky Lab doesn't have inappropriate ties with any government, which is why no credible evidence has been presented publicly by anyone or any organization to back up the false allegations made against the company," the company told AFP in an email.
Company founder and chief executive Eugene Kaspersky said he has repeatedly offered to present the company's source code to US officials for an audit, but has not been given the opportunity to do so.
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