The paper said that by firing Mr Comey, the President has cast doubt on further investigation into the Trump campaign's potential links to Russia, which could become "one of the biggest political scandals" in American history.
The FBI director was fired over his handling of the inquiry into Hillary Clinton's use of a private email server, the administration said.
But the Times points out Mr Trump praised Mr Comey when he told Congress he was reopening the investigation into Ms Clinton's emails.
"Of course, if Mr Trump truly believed, as he said in his letter of dismissal, that Mr Comey had undermined 'public trust and confidence' in the agency, he could just as well have fired him on his first day in office," the editorial said.
"Mr Comey was fired because he was leading an active investigation that could bring down a president. Though compromised by his own poor judgment, Mr. Comey’s agency has been pursuing ties between the Russian government and Mr. Trump and his associates, with potentially ruinous consequences for the administration."
The paper argued Mr Comey's inquiry "was the only aggressive effort to get to the bottom of Russia's ties to the Trump campaign."
It went on to call for the appointment of a special prosecutor to pursue the investigation.
"This is a tense and uncertain time in the nation’s history," the editorial said. "The president of the United States, who is no more above the law than any other citizen, has now decisively crippled the FBI’s ability to carry out an investigation of him and his associates.
"There is no guarantee that Mr Comey’s replacement, who will be chosen by Mr Trump, will continue that investigation; in fact, there are already hints to the contrary."
"The obvious historical parallel to Mr. Trump’s action was the so-called Saturday Night Massacre in October 1973, when President Richard Nixon ordered the firing of the special prosecutor investigating Watergate, prompting the principled resignations of the attorney general and his deputy."
It concludes: "But now, there is no special prosecutor in place to determine whether the public trust has been violated, and whether the presidency was effectively stolen by a hostile foreign power.
"For that reason, the country has reached an even more perilous moment."
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