The nine players were on their way to Colombo airport late Monday for the overnight flight when they were ordered to return, one of the team told AFP on condition of anonymity.
The rest of the squad are already in India taking part in a Test series. Sri Lankan cricket is in chaos and the national side has lost 21 one-day games this year and won just four.
Sports Ministry sources said Jayasekera was incensed that the players had been cleared to leave before he had given formal approval to the team selection.
A 1973 law gives the Sri Lankan sports minister the power to change national teams before they compete.
The ministry sources said Jayasekera may order at least two changes to the squad named by the Sri Lanka Cricket (SLC) board.
The nine players stopped from leaving were led by captain Thisara Perera who was only named last week.
The other eight are Upul Tharanga, Danushka Gunathilaka, Asela Gunaratne, Chathuranga de Silva, Sachith Pathirana, Dushmantha Chameera, Suranga Lakmal and Nuwan Pradeep. (Courtesy AFP)