"The explanation for this shocking move - that Mr. Comey's bungling of the investigation into Hillary Clinton's private email server violated longstanding Justice Department policy and profoundly damaged public trust in the agency - is impossible to take at face value," the Editorial Board of the New York Times said in an opinion piece.
By firing Comey, President Trump has "cast grave doubt on the viability of any further investigation into what could be one of the biggest political scandals in the country's history," the paper said.
"Mr. Comey was fired because he was leading an active investigation that could bring down a president," it said, referring to the ongoing probe into alleged Russian interference in the 2016 presidential election. It also noted that the outcome of the probe could have "potentially ruinous consequences for the administration."
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Trump will now appoint a new FBI director whose mission will include investigating Trump himself.
Trump's abrupt firing of Comey will intensify focus on the issue Trump has been so eager to dismiss - his knowledge of contacts between Michael Flynn and other associates and Russia, the opinion piece said.
"Trump has been digging a hole for himself from the beginning on Russia-related issues. It's an odd pattern of behavior. Trump may have done nothing improper involving Russia, but why does he act so defensive?," it asked.
"Frankly, the Comey firing is deeply troubling, reminiscent of (President) Richard Nixon's forcing out of special Watergate prosecutor Archibald Cox in 1973. Like Comey, Cox was investigating the president," it said.
"Now that Comey is gone there are two urgent priorities that Congress must insist on in its oversight role, the Los Angeles Times commented.
The move marked the most unpredictable moment of a presidency that through its first 100-plus days has been the least orthodox in memory, the channel said.
"The explanation for the move, which emerged into the stunned silence it caused, made little logical sense," it said.
"Removing the person charged with overseeing an investigation into a foreign country attempting to influence US elections by hurting one candidate (Clinton) and helping another (Trump) sends a chilling message up and down the federal bureaucracy -- not to mention the populace," it added.