The US president stunned Washington on by firing Comey who is investigating his administration's alleged links with Russia.
"This is absolutely a domestic matter for the United States, a sovereign decision by the US president which has absolutely nothing to do with Russia and cannot have anything to do with it," Kremlin spokesman Dmitry Peskov told journalists.
The US president stunned Washington by firing Comey, the man who leads the agency charged with investigating whether Trump campaign aides colluded with Russia to sway the November elections.
Asked how the change of leadership would affect bilateral relations, Peskov said "we hope that it won't affect them at all."
The head of the foreign affairs committee of the Russian senate Konstantin Kosachev earlier called Trump's firing of Comey "quite elegant" in comments to Interfax news agency.
"He removed a figure who was inconvenient for him using the same accusations that Trump's own opponents had previously presented against the FBI director," Kosachev said.
Trump's rival in the election Hillary Clinton blamed Comey for her defeat after he revealed just before the polls that he was re-opening a probe into Clinton's use of a personal email server while serving as secretary of state.