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Georgy Khelashvili, 32, who worked for the pardons commission, was found dead of a gunshot wound in his home on Friday night, police in Tbilisi said.
PM Zurab Zhvania, 41, was found dead in an apartment in the capital, poisoned by gas from a faulty heater.
It is not known whether the two deaths are linked.
Mr Khelashvili is thought to have shot himself with a hunting rifle borrowed from a neighbour.
"He left a note to his family and wrote the sort of things people write when they commit suicide," police spokesman Irankly Pirtskhalava said, quoted by Reuters news agency.
"Georgia will stand firm, and I hope I will stand firm because it is firmness that we need the most at present!"
Mikhail Saakashvili, Georgian President