No, Ciro Gomes has never been the target of PF investigations. This false news stems from a report published on September 2010 by Veja magazine that Ciro and his brother Cid Gomes were being investigated for fraud in bids in prefectures in the interior of Ceará.
Understand the context that originated the lie
The unsubstantiated indictment of the magazine was promptly denied by the Federal Prosecutor's Office and by the Federal Police's Regional Superintendence in Ceará, which in a press note dated September 1 stated that "investigations in progress [begun in September of 2009] did not reach any federal or state authority holding a privileged forum, nor did the Governor of the State of Ceará, CID FERREIRA GOMES, and federal deputy CIRO FERREIRA GOMES. "
Veja magazine was sued by Ciro Gomes because of the disclosure of this fake news.