White House correspondents of the Associated Press and Time magazine, who were among the select few invited to attend the gaggle, decided not to attend in protest.
Several top American media outlets, including The New York Times, CNN and The Los Angeles Times, which were among those press outlets critical of the Trump Administration, were not invited to Spicer's press gaggle.
The White House described it as an "extended gaggle".
The White House Correspondent's Association has lodged a protest with the White House on how the gaggle was being handled.
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Among those allowed in for the gaggle were Breitbart News, The Washington Times, NBC News and ABC News.
Earlier, in the morning, the White House updated its schedule telling reporters that Spicer would be holding an "extended pool" gaggle with reporters.
Those invited for the gaggle were sent a separate email in this regard.
As reporters gathered inside the press briefing room, many of them who had not received the email were asked to go back.
"We encourage the organisations that were allowed in to share the material with others in the press corps who were not. The board will be discussing this further with White House staff," it said.
"Nothing like this has ever happened at the White House in our long history of covering multiple administrations of different parties," New York Times executive editor Dean Baquet said in a statement.
"We strongly protest the exclusion of The New York Times and the other news organisations. Free media access to a transparent government is obviously of crucial national interest," he said.