Mr Brennan accused Donald Trump of withdrawing his clearance to distract from problems he is encountering and that he is following a playbook used by tyrants, despots and dictators.
But, he said the move would be a "powerful piece of evidence" for prosecutors as part of a pattern to demonstrate an intent to use presidential power in connection with the probe.
White House spokeswoman Sarah Huckabee Sanders announced the decision at a White House briefing Wednesday.
"Mr. Brennan has gone way over the line in my view and I think restricting his clearance, pulling his clearance makes sense to me", he said.More news: After raising tariffs on Ankara, US raps Turkish retaliation
"The only questions that remain are whether the collusion that took place constituted criminally liable conspiracy, whether obstruction of justice occurred to cover up any collusion or conspiracy, and how many members of "Trump Incorporated" attempted to defraud the government by laundering and concealing the movement of money into their pockets", said Brennan, who often has been highly critical of Trump on cable news talk shows.
But before the day was over, Trump had admitted what everyone already knew: that this was all about Brennan's piercing criticism and his role in launching the investigation into his campaign's possible involvement with the Russians in the 2016 election.
On Wednesday night, Trump sharing a variety of quotes from Fox News pundits bashing Brennan and the Obama administration on his Twitter feed, including one describing the former Central Intelligence Agency director as "a stain on the country".
Former CIA directors and other top national security officials are typically allowed to keep their clearances, at least for some period. "I really don't. And I don't think he's qualified to have one", Kennedy said, calling Brennan a "butthead". Trump said in the interview, a full transcript of which was not immediately published by the newspaper.More news: Remembering Aretha Franklin With 7 of Her Greatest Theatrical Performances
Graham added that he believed Trump should also strip Gen. Michael Flynn, Trump's former national security adviser, of his security clearance.
That directly contradicted a July 2017 statement from Trump Jr. - written with the consultation of the White House - that claimed the meeting had been primarily about adoption. "So, this is a risky precedent to set".
John Kennedy of Louisiana was more explicit in describing Brennan: "I think I called him a butthead and I meant it".
But at least two other Republicans were in favour of Trump's action.More news: Danny Cipriani in court over police assault outside Jersey nightclub
The president's comments were a swift departure from the official explanation given by the White House earlier Wednesday that cited the "the risks" posed by Brennan's alleged "erratic conduct and behaviour".