Kenyatta said people running government institutions will undergo the new tests to safeguard against "selfishness and greed."
"All heads of procurement and accounts in government ministries, departments, agencies and parastatals will undergo fresh vetting including polygraph testing, to determine their integrity and suitability," he said.
The tests will be concluded before the start of the next financial year, and those who fail will be suspended, he said. The government's fiscal year starts in July.
"You will hear of other tougher actions in the days to come," Kenyatta said.
One of Kenyatta's campaign promises when he was first elected for his first term in 2013 was to tackle corruption, but government agencies have been embroiled in several graft scandals.
"Many fear the procurement of the lie-detectors would itself be scandalous! Corruption is in the DNA of Kenya," Mohamed Yarrow tweeted.
Kenyatta acknowledged the rampant corruption, describing it as one of the main challenges facing the nation and urging citizens to join him in the fight.
"While the challenge may look huge because of the way corruption has become entrenched in some of our people today, we have to declare in unison that corruption in all its forms will be diminished from our country," he said.
One of East Africa's largest economies has had a series of corruption scandals in recent months.