Johnson said he made the decision in the last few days after a thorough review of the organization.
"I'm not going to get into a lot of specifics about why we're moving on from Mike," Johnson said on a conference call with reporters, including Manish Mehta of the New York Daily News.
Many questioned the timing of the firing, as the Jets moved on from head coach Todd Bowles in December but allowed Maccagnan to remain with the team through the hiring of Adam Gase, the beginning of free agency, and the draft.
"There's never a good time to make a decision like this," Johnson said, according to the New York Post's Brian Costello.
"This isn't a decision I could have made at the end of the season. I could with Todd. I couldn't with Mike," he said, according to Mehta.
On the same day that Bowles was let go by the Jets, Gase was fired as head coach of the Miami Dolphins after a 7-9 campaign. A week later, Gase was introduced as the new Jets coach.
Reports surfaced that Maccagnan and Gase clashed over the free-agent additions of Le'Veon Bell and C.J. Mosley. Johnson admitted the marriage between coach and GM "was not everything I was hoping for," according to Costello.
Nonetheless, he maintained that a power struggle was not the cause of Maccagnan's dismissal.
"This had nothing to do with Adam," Johnson said, according to Costello.
The CEO is seeking a "great, strategic thinker" and someone who can "collaborate well with the building" to fill the role of general manager, according to Dan Leberfeld of Jets Confidential.
In the meantime, Gase will hold the role on an interim basis.