"This is an attack on our country ... What we all stand for," he said.
Trump again blamed Attorney Gen. Jeff Sessions, saying Sessions made "a terrible mistake" in recusing himself last year from the investigation into Russia collusion and meddling in the 2016 presidential election. He also accused federal investigators of ignoring wrongdoing by Hillary Clinton's presidential campaign.
"This is a pure and simple witch hunt," he said.
The president learned of the raid on Cohen after it happened, but several hours before The New York Times first reported it Monday afternoon, a senior administration official told CNN.
Original report: The New York Times was the first to report on the raid.
Federal investigators seized a number of records, including documents connected to payments made to adult film star Stormy Daniels, the Times reported.
A phone, a computer and personal finance records were among the items investigators seized from Cohen's Rockefeller Center office, according to The Washington Post.
Cohen's lawyer said in a statement that special counsel Robert Mueller made a referral allowing federal prosecutors to obtain a search warrant.
CBS News is also reporting the FBI raided Cohen's New York residence, seizing documents and other materials.
Cohen's attorney Stephen Ryan called the raid "completely inappropriate and unnecessary," according to a statement released Monday afternoon.
"Today the U.S. Attorney’s Office for the Southern District of New York executed a series of search warrants and seized the privileged communications between my client, Michael Cohen, and his clients. I have been advised by federal prosecutors that the New York action is, in part, a referral by the Office of Special Counsel, Robert Mueller,” Ryan said.
The raid "resulted in the unnecessary seizure of protected attorney client communications between a lawyer and his client," Ryan said in the statement.
Ryan also called the raid wrong. "Mr. Cohen has cooperated with all government entities, including providing thousands of non-privileged documents to Congress and sitting for depositions under oath."
Mueller's office refused to comment on the raid, CNN reported. It's unclear exactly what investigators were looking for or exactly which documents and materials they may have seized.
Meantime, the president has been watching the news on TV, a White House official told CNN. It's unclear if Trump has spoken to Cohen about the search.
Cohen has said he paid Stormy Daniels $130,000 from his personal account in 2016 just before the presidential election in exchange for a non-disclosure agreement that prevented the exotic film star from publicly discussing the alleged 2006 affair with Trump. The White House has repeatedly denied Daniels' allegations of an affair.
After months of keeping quiet, Trump finally commented on the situation Thursday, saying he was unaware of Cohen's payment to Daniels. Cohen has also maintained the president did not know about the payment.