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The KRA officials were conducting routine checks at Consolbase Limited in Mombasa when they came across the documents hidden away in one of the containers.
According to Mr Benson Chacha, a KRA manager, the 40ft container was from the United Arab Emirates and had been imported by a company called Machine Technology.
"We found goods that had not been declared upon entry. These included identity cards and passports meant for Somali republic and finger print machines," said Chacha.
"The fake passports and IDs were hidden between boxes of computers and CCTV cameras to make it difficult to find them in a search," he added.
He said the container would remain under their custody while they conducted investigation to establish the purpose of the items.
The quantity of the consignment was yet to be established as police from the anti-terror unit and KRA officials were still sifting through the material.
Port Deputy OCPD Benjamin Rotich said although they suspected the assorted goods could be linked to the Al Shabaab terror group, the truth could only be established once investigation was completed.
Elsewhere, a wave of grenade attacks killed a child and wounded nine other people in the Somali capital.
At least five attacks hit different parts of the city, said police.
It was a hand grenade thrown into a house as people watched a football match between England and Sweden that killed the boy.
"We are still confused about the meaning of this attack," said Daud Hussein, the owner of the house in the Seypiano district of the city.
"We were simply watching football when the explosion hit the house, a young boy was killed and four others injured," he said.
"Everybody was excited to be watching the game, and no one expected that such a horrible incident was about to happen," Mohamed Black, a witness said.
"I’m lucky to survive but a friend of mine was among the injured."