Bee used an offensive slur when attacking Ms Trump over the Trump administration's immigration policy.
Mr Trump called it a "double standard" that her show was not cancelled like Roseanne Barr, who lost her sitcom after she posted a racist tweet.
Bee has apologised, saying she "crossed a line" with the vulgar phrase.
In his tweet, the president appeared to suggest that it was unfair that Bee did not lose her show as Barr had.
Barr came under fire earlier this week for making a racist comment about former Obama aide Valerie Jarrett. She compared Ms Jarrett, an African American, to an ape.
Disney, the parent company of ABC TV network, on Tuesday dropped Roseanne's rebooted '90s sitcom amid a ferocious online backlash over her racist tweet. Disney chief executive Bob Iger apologised to Ms Jarrett over the incident.
In a now-deleted Tweet, Barr said she implored ABC not to axe her sitcom.
"I begged them not to cancel the show. I told them I was willing to do anything," she wrote, adding that she asked for "help in making things right".
Mr Trump has not condemned Barr's remarks, but criticised Mr Iger for the "horrible" things said about him by the entertainment conglomerate's television personalities.
What did Bee say?
On her political commentary show Full Frontal, Bee attacked the president's daughter over a long-standing US policy of separating undocumented immigrant children from their families.
Presenting Obama-era photos of such young people sleeping in cages, Bee said: "Tearing children away from their parents is so evil, it's the inciting incident in almost every movie we've ever cared about."
She said Ms Trump had been "oblivious" recently to post an Instagram photo of herself hugging her child.
She then called Ms Trump a "feckless [expletive]", employing an offensive term for part of the female anatomy.
Bee urged the first daughter to confront her father about the policy.
Why did Ivanka's mother and child photo spark backlash
"He listens to you," she said. "Put on something tight and low-cut and tell your father to [expletive] stop it. Tell him it was an Obama thing and see how it goes, OK?"
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