They embraced their wives, children and others who received them and thanked the government for securing their release.
Juma told reporters that Njoroge and Shamalla had to be rushed to the hospital as their health had deteriorated.
"The family of the detained pilots have suffered great emotional and psychological distress during the unacceptable long period of detention. We are leaving straight for the hospital," she said.
"They have both come back to their families emaciated and severely ill."

Captain Kennedy Shamalla with his family at Wilson Airport in Nairobi following his return from South Sudan, February 20, 2018. /PATRICK VIDIJA
Juma condemned the capture and urged Kenyans to exercise extreme caution especially while visiting countries undergoing unrest.
Oil-rich South Sudan has been riven by civil war since 2013. The conflict has displaced a third of the population, shut down most of the oil production and wrecked the economy.
"We condemn the capture and detention of pilots in the strongest terms possible," the Minister said.
South Sudanese rebels released the two Kenyans after receiving compensation for the family of a civilian killed when their plane crashed last month.
Their plane came down in Akobo, in the Greater Upper Nile region in early January, and the rebels asked for compensation for the family of a woman who was killed, and for others who lost livestock.
Lam Paul Gabriel, deputy spokesman of the rebel SPLA-IO said Sh10.9 million had been paid.
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