Licensed civilian firearm holders have up to March 18 to acquire special identification cards introduced by the Interior ministry.
Interior CS Fred Matiang'i on Monday said the cards will be fitted with chips that will contain the personal details of holders.
He spoke in Mombasa during a meeting with regional coordinators, regional police commanders, county commissioners and county police commanders from across the country.
The order comes amid an ongoing case in which the challenging a directive by Matiang'i that requires all civilian gun owners be vetted afresh.
In the suit, the association said calling for fresh vetting was unfair, citing the Fair Administrative Actions Act.
The court temporarily halted the vetting in December.
Matiang'i has said there are many unaccounted for firearms in the wrong hands.
"We collect a lot of cartridges but are not able to trace the firearms," he said.
"These chips will help us be able to trace and track them."
Last Friday, the state announced plans to arm guards to improve security
following the Dusit attack on Tuesday last week.
The attack claimed 21 lives.
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Private Security Regulatory Authority director general Fazul Mahamad said the government will vet all security guards before arming them.
Security companies will also be vetted to weed out criminals in the industry before licensing private guards to own guns.