Publisher Trinity Mirror said on Wednesday that the Daily Mirror's Richard Wallace and Sunday Mirror's Tina Weaver would leave with "immediate effect".
Lloyd Embley, current editor of The People, has been appointed to oversee both papers in the move to a seven-day publishing model.
New senior editorial roles will be created for the Daily Mirror and Mirror (Saturday and Sunday) respectively.
NUJ general secretary Michelle Stanistreet said that the "shock" decision to fire Wallace and Weaver was done "without any consultation or agreement with staff".
In a statement, she added that it was a sign that Trinity Mirror is a "company in crisis".
Stanistreet slammed the Trinity Mirror board for allowing Sly Bailey, the company's former chief executive, to push through the "drastic" merger before announcing her departure from the firm earlier in the month.
"It says a lot about the board of Trinity Mirror that they have allowed chief executive Sly Bailey, finally on her way out after presiding over stupendous decline, to push such drastic measures through," said Stanistreet.
"The statement from the company tries to dress up this last hurrah as a leap into a brave new world of multimedia publishing - the reality is that these cuts and the weakening of the titles' identities will be a further blow to resources and quality journalism from a lame duck chief executive whose monumental lack of vision has seen the company's fortunes plummet."
Stanistreet added: "Half of all jobs across the entire group have already been axed, the company's strength has ebbed away yet executives have consistently attacked its assets - journalists and the quality journalism they produce."
Even though the NUJ does not have formal recognition rights yet at Trinity Mirror's national titles, Stanistreet said that the union would be holding a meeting with members across the papers to discuss their response to the merger.