Mr Erdogan said the 1923 Treaty of Lausanne was a defeat for Turkey as it "gave away" islands to Greece.
Greek Defence Minister Panos Kammenos warned Turkey not to pursue "dangerous paths".
Tensions over a disputed Aegean islet in 1996 brought Greece and Turkey to the brink of war.
Since then, relations between the neighbours have eased.
Speaking in Ankara on Thursday, Mr Erdogan said the Treaty of Lausanne, which forged the modern borders between Greece and Turkey, was essentially a defeat for Turkey.
"We gave away islands to Greece that we could reach with a shout. Is this victory? Some tried to trick us into believing that Lausanne was a victory," he said.
"Those who sat at that table did not do right by that treaty. Now, we suffer its setbacks."
'Danger to relations'
Mr Erdogan's remarks angered both the Greek government and the Turkish opposition.
"Efforts to cast doubt on international treaties lead to dangerous paths," said Mr Kammenos on Friday, urging Turkey not to "pursue" those paths.
Greece's Prime Minister Alexis Tsipras said questioning the treaty was "dangerous to relations between the two countries and to the broader region", his office said.
Turkey's main opposition CHP party - whose late leader negotiated the treaty - said Lausanne had reversed the tough conditions of a previous treaty that had been negotiated by leaders of the Ottoman Empire.
CHP leader Kemal Kilicdaroglu said Lausanne was "Turkey's deed" and questioned why Mr Erdogan had raised the issue while there was "unemployment, corruption and people chasing after their lives" across Turkey, the Hurriyet Daily News reported.
Mr Erdogan came to power in 2002 and has become known for his authoritarian approach.
He spent 11 years as prime minister before becoming Turkey's first directly-elected president in August 2014.