"I thought he was a dick yesterday," Halperin said on Thursday's show during a discussion about Obama's news conference the day before.
Halperin, a Time magazine editor at large, quickly apologised on the air and in a statement. MSNBC suspended him indefinitely and Halperin said he believed the action was appropriate.
Halperin had prefaced his remark by asking, "Are we on the seven-second delay?" and said after that "I hope it worked."
It didn't.
The reference was to a brief delay in a TV show transmission that gives a producer the chance to quickly silence an offending remark before it goes out over the air. MSNBC said "Morning Joe" had the delay, but a producer pushed a wrong button and Halperin's statement wasn't edited out.
MSNBC said Halperin's comment was "completely inappropriate and unacceptable" and apologized to the president.
"I want to offer a heartfelt and profound apology to the president, to my MSNBC colleagues, and to the viewers," Halperin said. "My remark was unacceptable, and I deeply regret it."
White House spokesman Jay Carney, a former Time magazine bureau chief in Washington, said Halperin's comment was an inappropriate thing to say about any president, and that he had expressed this sentiment to network executives.
Carney had no comment on MSNBC's decision to suspend Halperin.
Time magazine spokesman Daniel Kile said the company had told Halperin his behaviour was unacceptable.