The Office of the President and Cabinet (OPC) said in a statement Mutharika will be represented at the funeral on Wednesday at Chikolosa village, TA Kanduku in Mwamza, by Homeland security Minister Nicholas Dausi.
Khonje was Speaker during the one-party era from 1975 to 1987.
Dausi, who is Mwanza Central MP, described the death of Khonje as a big brow to the family, Mwanza district and Malawi as a whole, adding that Khonje was a calm and humble personality.
Born on December 6, 1923, Khonje, a secondary school teacher by profession, joined politics in 1971.
Khonje went to Matandani and Malamulo Seventh Day Adventist Schools before qualifying for Cambridge O-level through correspondence.
He attended Moray House College of Education in 1962 and returned to Malawi two years to launch a career as teacher at various secondary schools up to 1971 when he became MP.
He quit MCP in 1993 and joined United Democratic Party (UDF). He retained his seat for Mwanza central constituency in the first post independent multiparty general election in 1994.