News of the beheadings came as six people were killed in two bus bombs in the southern Philippines.
Brigadier-General Glicerio Sua said the bodies had been found on Basilan island at the camp where the hostages - mostly Filipino school children - had been held by Abu Sayyaf.
The armed forces rescued 15 of the hostages earlier in the week, but four others were found dead.
News of the beheadings came as six people were killed in two bus bombs in the southern Philippines.
The army blamed the blasts on the country's largest Muslim separatist group, the Moro Islamic Liberation Front (MILF) - despite the guerrillas' announcement of a 48-hour ceasefire.
Army scout rangers found the bodies of the two teachers with their hands tied behind their backs in a shallow grave at the camp in Basilan. They had been abducted, with 27 others, on 20 March.
Abu Sayyaf has threatened to behead two members of a separate group of 21 mostly-foreign captives on Jolo island if the military does not remove its troops from around its camps.
Supplies of food and medicine are ready to be delivered to the kidnappers, a mission which negotiators hope will allow a resumed dialogue with Abu Sayyaf.
The hostages were seized from the Malaysian resort island of Sipadan on 23 April. Most are suffering from stomach illnesses, and one has a urinary tract infection.
Government negotiator Nur Misuari has said he will meet Philippine President Joseph Estrada on Sunday, but added he had not yet received the rebels' written demands.
Collaboration
On Saturday, the government accused the MILF of collaborating with Abu Sayyaf.
Defence Secretary Orlando Mercado said the two groups were working together to fight for a separate Muslim state on the main southern island of Mindanao.
"We all know that all these (incidents) in Mindanao are concerted actions," he said.
The bus attacks on Saturday afternoon followed about 10 other grenade and bomb attacks elsewhere in Mindanao since Friday night.
At least four people died and 22 were wounded when the first bomb went off on a bus as it entered Surigao, radio reports quoted police as saying.
Two more people were killed and at least 10 others wounded when another device exploded on a bus in Butuan. A larger bomb was found in a third bus and defused.
The BBC's John McLean in Manila says bus companies are often targets of extortionists, and the MILF always denies involvement in such attacks.
Truce ignored
The MILF declared a unilateral weekend truce from Saturday morning - a week after it had abandoned peace talks and launched a series of attacks which left at least 42 dead.
Mr Mercado said the government would not accept the ceasefire unless both the MILF and Abu Sayyaf lowered their arms and released the hostages.
"We're not talking about surrender. If they lay down their arms we can talk," he said in a national broadcast.
Fighting has continued between government troops and MILF guerrillas on the key Narciso Ramos highway in the south of Mindanao.
The government says the rebels must clear the road before any truce can be forged. However, the MILF argues that its main base includes parts of the highway.
A MILF official insisted the group was observing its ceasefire, but the military had continued its offensive.
Armed forces chief General Angelo Reyes admitted that the military had lost 40 men and suffered almost 150 injured in the fighting but did not give figures for MILF casualties.
Mr Estrada said he hoped the truce would lead to a resumption of talks.
"I offer peace to those who want peace. But I promise to defeat those who want war," he said.
Mindanao, 800km south of the capital, Manila, is home to most of the country's five million Muslims. The Philippines is a mostly Catholic country.