There was "broad scope" to improve the CFP, said Mrs Bonino during talks with fishermen and industry leaders at Brixham, south Devon.
She made similar overtures to fishing interests at Newlyn, west Cornwall, where she said discussions could herald a "new start" in Europe's relations with the United Kingdom industry.
Mrs Bonino was welcomed to Brixham by banner-waving supporters of the Save Britain's Fish campaign - which wants the UK to dump the CFP and take control of British waters up to 200 miles.
Mrs Bonino said it was up to Parliament to decide whether to withdraw from the CFP, which British fishermen feel is unfair. But she added: "I strongly believe it is better to improve the existing CFP."
Talks involving other European member states to come up with new ideas for reform were of the "utmost importance", she said, adding: "I do not think the CFP is perfect, but I do think there is scope to improve it."
And she welcomed the Government's White Paper on Europe, which spoke of remaining in the CFP but looking for improvements to it.
But the chief executive of the South West Fish Producers' Organisation, Jim Portus, said afterwards that Mrs Bonino had made clear the industry's answer lay with Parliament, which is what the industry had believed for some time.
"So until we get our Parliament to make policy decisions favourable to the fishing industry, I do not see any point in arguing who is right or wrong in Europe," he said.
He did not believe the European discussions she suggested would result in any long-term improvement for British fishermen. However, it was a worthwhile visit for Mrs Bonino, who had been living in a state of "complete ignorance" of the concerns of the UK fishing industry, said Mr Portus.
Fishermen are also bitter about the armada of foreign-owned, UK-registered vessels fishing on the British quota.
Mrs Bonino said there were ways of reducing the impact of "quota-hoppers" now, and she would give "all legal assistance".
The Cornish Fish Producers' Organisation chief executive, Mike Townsend, said "radical changes" were needed in the CFP, but he had taken "some comfort" from the meeting.