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Detectives from Interpol and other agencies apprehended Ephathus Gitonga based on information in an intelligence report.
Port DCIO Juliana Muthini said he was being held at Port police station and will be taken to court amid a search for other suspects.
“This is a serious offence. We are working round the clock to ensure the Port is safe,” she said.
Senior Kenya Revenue Authority officials are being investigated in connection to the Tuesday seizure.
The multi-agency team launched the probe in a crackdown on customs officials and clearing agents who might have colluded to sneak out two containers containing the trophies.
The two tonnes of smuggled ivory were impounded after a shipment en route to Cambodia was recalled, following intelligence that it contained illegal cargo.