She added that State agreed with preliminary findings of "gold standard" OSCE monitors that Russia's election was "overly controlled" and "lacked genuine competition".
The Organization for Security and Co-operation in Europe (OSCE) said there had been no real choice in Russia's presidential election and complained it had been marked by unfair pressure on critical voices.
"DO NOT CONGRATULATE", it reportedly said in all caps. State Department spokesperson Heather Nauert explained Tuesday that the call was merely "protocol" and "standard" - referring reporters to the White House readout.
He also described a call he made to Putin to congratulate him on his reelection.
Tensions between the Moscow and the West continues to mount amid global concern over a nerve gas attack on a former Russian double agent living in England and questions about meddling in elections and attempting to hack infrastructure in the U.S.
White House press secretary Sarah Sanders said that the White House believes maintaining a relationship with Putin is worth it, despite some outstanding issues. "And by doing so with Vladimir Putin, President Trump insulted every Russian citizen who was denied the right to vote in a free and fair election to determine their country's future".
Other Western leaders also called to congratulate Putin.
They spoke after Washington slapped a new round of sanctions against Moscow created to punish Russians responsible for attempts to interfere in the 2016 presidential elections.
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The president said he and Mr. Putin would also discuss tensions in Ukraine, Syria and North Korea, among other issues.
Meanwhile, a US Senate committee has released its first draft recommendations on how to prevent hacking of US elections, after spending more than a year investigating claims of Russian attempts to target the voting system during the 2016 campaign.
Donald Trump was given stern instructions from his national security team - "DO NOT CONGRATULATE" Vladimir Putin on his recent re-election that came after Russian Federation launched an alleged attack in the United Kingdom that left a former spy dead. His tone has at times been at odds with his administration, which has taken stronger actions to counter Russian aggression, including Trump's authorisation of new sanctions against Russia and additional support Ukrainian troops in their fight against Russian-backed forces in Crimea.
Earlier on Tuesday, Russian Deputy Foreign Minister Sergei Ryabkov said he hoped Putin's win would persuade some USA politicians to stop isolating Russia and said Moscow was open to dialogue with Washington, the RIA news agency reported.
Trump, who vowed to improve relations with Russian Federation on taking office 14 months ago, is under pressure from Congress to take a tougher stance on Putin, his inner circle and scores ofRussian oligarchs.
Trump did tell reporters that he would meet with Putin in the "not too distant future".
Sanders declined to pass judgment on those elections Monday.