The former CEO of Exxon Mobil told his Senate confirmation hearing the intelligence report on Russian tampering "clearly is troubling".
His comments came after Senator Marco Rubio pressed Mr Tillerson to admit Mr Putin's role in the cyber-breach.
Mr Tillerson's reported good ties with Mr Putin have alarmed some in the US.
The 64-year-old former corporate titan, who has never worked in government, faced tough questions from the Senate Foreign Relations Committee on Wednesday.