Cohen and his wife as of April owned or controlled a total of 54 medallions in New York and Chicago as of April.
The Journal additionally reported that prosecutors are investigating whether employees of a bank improperly allowed Cohen to get loans "for which he didn't provide adequate documentation."
And authorities are probing whether Cohen overstated his income on applications for loans and other refinancing efforts.
The article said prosecutors have subpoeaned Cohen's former accountant, Jeffrey Getzel, who had also worked as a accountant for Evgeny Freidman, a manager of taxi medallions who pleaded guilty this year to tax fraud.
Freidman is cooperating with federal prosecutors, according to the Journal.
Lanny Davis, a lawyer for Cohen, did not immediately respond to a request for comment from CNBC.
Cohen has been under investigation by prosecutors from the Office of the U.S. Attorney for the Southern District of New York since at least earlier this year.
In April, FBI agents raided his office and residences in New York and seized hundreds of thousands of files.
Among those files was evidence relating to a $130,000 hush-money payment Cohen gave porn star Stormy Daniels shortly before the 2016 presidential election.
Daniels, whose real name is Stephanie Clifford, has said the money was in exchange for her agreed-upon silence about an affair she claimed to have had with Trump in 2006.
The White House has denied that Trump had sex with Daniels. But Trump has acknowledged reimbursing Cohen for the payment to her.
Authorities are investigating whether that payment or the way it was handled constituted a violation of federal election law.
Prosecutors also are looking at a payment the publisher of the National Enquirer made in the months before the election to Playboy model Karen McDougal, who also claims to have had an affair with Trump. The supermarket tabloid never ran her account of that alleged relationship, which Trump has denied ever occurred.
Cohen secretly taped a conversation he had with Trump in 2016 discussing possibly buying the rights to McDougal's story.
The recent revelation of that tape's existence led Trump's current lawyer Rudy Giuliani to call Cohen a "scoundrel" and "a liar."