WASHINGTON — The federal government moved on Wednesday to wipe from its computer systems any software made by a prominent Russian cybersecurity firm, Kaspersky Lab, that is being investigated by the F.B.I. for possible links to Russian security services.

The concerns surrounding Kaspersky, whose software is sold throughout the United States, are longstanding. The F.B.I., aided by American spies, has for years been trying to determine whether Kaspersky’s senior executives are working with Russian military and intelligence, according to current and former American officials. The F.B.I. has also been investigating whether Kaspersky software, including its well-regarded antivirus programs, contain back doors that could allow Russian intelligence access into computers on which it is running. The company denies the allegations.

The officials, all of whom spoke on the condition of anonymity because the inquiries are classified, would not provide details of the information they have collected on Kaspersky. But on Wednesday, Elaine C. Duke, the acting secretary of Homeland Security, ordered federal agencies to develop plans to remove Kaspersky software from government systems in the next 90 days.

Wednesday’s announcement is the latest instance of the apparent disconnect between the Trump White House, which has often downplayed the threat of Russian interference to the country’s infrastructure, and front-line American law enforcement and intelligence officials, who are engaged in a perpetual shadow war against Moscow-directed operatives.