Pothas and several other players then refused to travel to Pakistan for the final Twenty20 international of the tour, citing security concerns.
After six months at the helm he was replaced by former Sri Lanka Test batsman Chandika Hathurusingha, who was named head coach in December.
"After two incredible years with Sri Lanka cricket, this is the right time for me to move on to other opportunities, which will allow me to spend quality time with my young family," Pothas said in a statement issued by the cricket board.
"It has been an honour and a privilege to be involved with Sri Lanka.
"It has given me the opportunity to learn and improve as a coach as well as to contribute to a very talented bunch of players. It will always hold a special place in my heart.
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