He added, "But we have a responsibility to engage our elected officials to work constructively and advocate for policies that improve people's lives and protect our environment ."

In an emailed statement to CNBC, Dimon said, "I absolutely disagree with the Administration on this issue."

Jamie Dimon, chairman and CEO of JPMorgan Chase, speaks at the Economic Club of Washington September 12, 2016 in Washington, DC.

Dimon is one of the CEOs to participate in White House councils and in his statement he did not indicate if he would remain in that post.

On Thursday, Disney CEO Robert Iger said he quit the business advisory council over the decision, while Tesla and SpaceX CEO Elon Musk also said he'll leave his positions on presidential councils.

The president said he would start talks to re-enter the agreement, but with terms that he called a more "fair" deal to his country. His comment was rebuked by several European governments.

Many business leaders in the U.S. said they were disappointed by, or disagreed with, the decision, including Apple chief Tim Cook, Google's Sundar Pichai and Facebook's Mark Zuckerberg.

Last month, at JPMorgan's annual shareholder meeting, Dimon had urged the business community and the administration to work together to find meaningful solutions to critical issues confronting the U.S.

In response to a question on Trump's tighter immigration policy, Dimon had said, "He is the president of the United States. I believe he is the pilot flying our plane. I would try to help any president of the United States because I am a patriot."

— CNBC's Dawn Giel contributed to this report.