The light aircraft crashed into an unoccupied house at 3pm (1200 GMT) near Narok town, about 220km southwest of Nairobi, Charles Otieno, a police spokesman, said earlier.
The plane was operated by Nairobi-based Flight Trade Limited and was bound for Kericho, Kenya's tea-farming capital in the Rift Valley.
"The plane came down on an unoccupied house and disintegrated, killing all four occupants," Patrick Wambani, the Narok district police chief, told Reuters news agency.
Both politicians were members of the Orange Democratic Movement (ODM) party.
The ODM entered a power-sharing government with Kibaki's party after disputed elections in December caused widespread violence.
Kibaki's statement did not mention who would succeed the ministers but it is almost certain that their replacements will be drawn from the ODM under terms of the power-sharing agreement.
The president said that flags will fly at half mast until the two politicians are buried.
"This is unbearable news of these deaths," Salim Lone, a spokesman for Raila Odinga, the prime minister, told The Associated Press news agency.
Kones was a five-term member of parliament and was first elected in 1988, after a career as a teacher and manager at a produce firm.
He held several other ministerial posts throughout his public career.
Laboso, a first term politician, was among the small number of women elected to Kenya's National Assembly.
Laboso campaigned against the cultural practice of female genital mutilation in her Kipsigis tribe.