The bodies of the two ethnic Tamil men were found Saturday in Ratnapura district, about 60 miles southeast of the capital, Colombo, Red Cross Director General Neville Nanayakkara said.
Nanayakkara said the two men, S. Shanmugalingam and K. Chandramohan, had been in Colombo to attend a two-day workshop.
They were waiting at the capital's train station Friday for a train home, along with four other colleagues from the eastern town of Batticaloa, when they were approached by men claiming to be police, he said.
Nanayakkara said the men, dressed in civilian clothing, checked identity cards and then took Shanmugalingam and Chandramohan away, saying they needed to be questioned.
The other four insisted they too would wait at the police station until the questioning was over, but the men drove off in a white car, he said.
"Yesterday, I saw some television reporting that two bodies were found and I had my doubts, so I sent two officers today to Ratnapura hospital and they identified the bodies," Nanayakkara said.
"They had been shot through the head," he said.
Hundreds of people have been abducted in the capital and the island's north and east in recent months amid a deepening conflict between ethnic Tamil rebels and the government.
The killing is the worst attack against aid workers since the massacre of 17 local employees of the French charity ACF, or Action Against Hunger, in August.