The move has resulted in the port finding it difficult to accommodate more cargo.
He said some of vessels were not calling over due to the congestion which has caused delays.
General Ratnayake said as a result some of the ships were bypassing Colombo and heading to ports in Singapore, India and Bangladesh.
He said for a day they were handling 500 containers for exports while earlier they had handled 800 to 1000 a day.
He said essential food items were arriving in the country uninterrupted and steps were being taken to clear the goods without delay.
Customs Director General Retd. Maj. Gen.Vijitha Ravipriya said that though seven of its employees were afflicted with COVID-19, they were continuing to maintain round-the-clock services to clear goods.
The activities at the Colombo Port slowed down after 14 of its employees were afflicted with COVID-19 and several others were sent on quarantine.
-The Sunday Times