The actions escalated Trump's efforts to restrict news coverage by journalists he finds objectionable.
Trump said on Friday he would ban both organisations and Politico from the White House because of their coverage, calling them "fake news" outlets.
CNN issued a statement saying it stood behind its reporters.
"We will not be deflected from our duty to hold the government and other public bodies to account," it said.
The statement was shown on the air on Saturday morning before senior White House reporter Betsy Klein began to report on her ban.
MSNOW White House correspondent Akayla Gardner was also turned away and her entry badge confiscated, she said on air on Saturday morning.
She noted she had walked through two gates successfully but once she got to where her badge needed to be scanned, an officer told her it was disabled and asked her to hand it over.
He said the decision "was above him," she said.
An MSNOW producer was able to get in but a photographer's badge was also disabled, Gardner said.
Politico journalists typically are not at the White House on Saturdays.
Trump wrote on his social media site on Friday that effective immediately, "I am banning" CNN, MS NOW and Politico "from the White House as a result of their constant 'reporting' FAKE NEWS!".
Minutes later, speaking at an event in the Oval Office, Trump was asked to explain his statement.
"Because they're fake news," he said.
"You get so tired of reading and seeing fake news. When you look at CNN, it's just fake. That's why their ratings are no good. When you look at MS NOW…, it's fake news."
"And when you look at Politico ... the stories they wrote are fake. So there's a lot of news and there may be others to join them, and maybe they can get better," he said. "But our country has to have honest news."
In his second term, Trump and his administration have upped the ante and punished certain media outlets both in the courtroom and through regulatory action.
Trump has also criticised individual reporters in person or over social media.
The move follows the president's decision last year to bar Associated Press reporters from the Oval Office, Air Force One and other events in retaliation for the news outlet's decision not to follow his lead in changing the name of the Gulf of Mexico.
The AP said that it would note when appropriate that Trump had ordered it renamed the "Gulf of America".
