The meeting, which lasted nearly two hours, comes after officials in Moscow initially said Putin would not meet with Tillerson during his first visit to Russian Federation, later hedging to say a sit down was possible. The Kremlin had previously declined to confirm Putin would meet Tillerson, reflecting the renewed tensions.
The talks got off to a frosty start, with the Russian politician branding the American cruise missile strike "illegal" and criticising "confusing and sometimes openly contradictory ideas" from the Trump administration on the US-Russia relationship and global issues.
Putin's assessment comes a day after the Trump administration accused Russian Federation of orchestrating a "disinformation campaign" to cover up the chemical attack in Syria's Idlib province.
"There is a low level of trust between our two countries", Mr Tillerson said.
The text also condemned the reported use of chemical weapons and demanded a speedy investigation.
The United States responded to the gas attack by firing 59 cruise missiles at a Syrian air base.
Tillerson also held what he called a "productive" two-hour long meeting with Russian Foreign Minister Sergey Lavrov.
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Meanwhile Putin, who had an infamously icy relationship with President Barack Obama, said in an interview that U.S. - Russian relations have actually gotten worse since Trump took office.
The foreign ministers from Russia, Syria and Iran, meeting Friday in Moscow, said any further unilateral action by the U.S.in Syria would be met with "grave consequences" and pose a danger to the entire world.
The spokesman, Dmitry Peskov, told a conference call with reporters on Thursday that the tone of the meeting had been "fairly constructive".
"With all the existing problems, both objective and artificially created ones, we still have quite a few prospects for joint work", he said.
"It's deplorable, and we regret what is going on, but we can do little except asking to back accusations with facts", Mr Lavrov said.
Last week's US strike on a Syrian air base dominated talks, with both sides still not seeing eye-to-eye.
He said political settlement is the only viable way to resolve the Syrian issue and called for the worldwide community to continue support for the United Nations to play the lead role.
"Putin is backing a person that's truly an evil person". Trump said in a note on Twitter. "And I think it's very bad for Russian Federation", he said in and interview with Maria Bartiromo airing today on Fox Business Network. "How do you know that?" he said.