Midfielders Frank Banda and Davie Banda were expelled on Monday after the technical panel discovered that the two had sneaked out of the team's training camp on Sunday night.
Team Manager, Stewart Mbolembole told BBC Sports that the technical panel decided to act swiftly. "We got a report that the two left camp on Sunday night and only returned in the early hours of Monday morning," he said.
"As a national team we insist on discipline so a meeting of the technical panel decided to send them home."
The incident followed the expulsion last week of another midfielder, Peter Pindani, due to club indiscipline.
Coach Kinnah Phiri said the absence of the three players will not heavily affect the team's preparations for the Cecafa Challenge Cup.
"I have capable replacements and - who knows - the absence of the indisciplined players will give a chance for new talent to shine."
Malawi, who have been guests at the tournament for the past three years, have been drawn in Group C alongside Rwanda, Zanzibar and Somalia.
Kenya's Harambee Stars have been pooled in Group "A" alongside hosts Uganda, Ethiopia and South Sudan. The Kenyans take on Uganda Cranes in their opening fixture on Saturday at Namboole Stadium.