The landslide happened on Tuesday night outside a gold mining site in the town of Maco in the province of Davao de Oro, where the buses were picking up employees, mining operator Apex Mining APX.PS said in a separate statement.
Edward Macapili, provincial disaster official, said in a phone interview that the two buses were carrying a total of 27 passengers, and it is likely they have been included in the 46 recorded missing.
Based on the account of Apex Mining, there were four 60-seater buses and one jeep with a 36-passenger capacity waiting for the outgoing employees of the mine before the disaster struck. One bus had left, while the rest were still waiting when the landslide occurred.
As of 11:30 a.m. (0330 GMT) on Wednesday, 62 Apex Mining employees have been accounted for, while the whereabouts of 45 other employees were still being traced, the company said.
More than 700 families in affected areas have been evacuated, Maco's disaster agency said in a separate statement.
A northeast monsoon and a trough of low pressure brought rains to the southern Mindanao region over the Jan. 28-Feb. 2 period, resulting in deadly floods and landslides, data from the national disaster agency showed.