John Longworth, director general of the British Chambers of Commerce, made his remarks in a speech earlier this week, going beyond the BCC's official position of neutrality.
The BCC refused to comment on the FT's report when contacted by AFP.
Longworth gave a keynote speech on Thursday in which he said the referendum was a choice between the "devil and the deep blue sea".
He later told Sky News: "I actually went on in my speech beyond what the Chambers of Commerce believe, to talk a little bit about what my analysis of the evidence has been.
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The FT reported that Longworth "has been suspended after he took to the airwaves to call for Brexit -- against the wishes of most of its members".
In a statement issued before reports of the suspension arose, the BCC said it "will not be campaigning for either side ahead of the EU referendum".
But a spokesman did acknowledge that Longworth "has been very clear where his remarks reflect his personal assessment, rather than the position of the BCC".
The country's car industry this week publicly backed the remain campaign while small business owners have spoken out against the cost of Brussels red tape.