The scanners can detect radioactive materials inside containers.
The Colombo port scanning was prompted by the release of radiation into the atmosphere from Japan's nuclear power plant at Fukushima which was damaged when an earthquake and tsunami caused power shortage across northern Japan.
Japanese authorities have also detected slightly higher than normal levels radio activity in vegetables and milk in areas near the plant, but said it was not a danger to human health.
"The SLPA along with the Sri Lanka Customs and Atomic Energy Authority have taken immediate precautionary measures against possible radiation threats to the country due to the recent explosions at the Fukushima nuclear plants in Japan," the port said in a statement.
"All cargoes arriving from Japanese ports from and around the affected areas are subjected to radiation checks at the Port of Colombo.
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In-bound containers and motor vehicles are driven through radiation scanners installed under the 'Mega Ports Initiat