Guzman was recaptured on Friday, six months after staging a spectacular prison break through a tunnel in his cell floor. While on the run, Guzman met secretly with Penn at a jungle hideout - a move the government says was "essential" to his capture.
Penn published an article in Rolling Stone magazine on Saturday in which he quotes Guzman boasting about his drug shipments and laundering money through major Mexican and foreign companies.
READ: 'El Chapo' in his own words
"Its a lie, absurd speculation from Mr Penn," Juan Pablo Badillo, one of a team of Guzman lawyers, told Reuters in an interview on Wednesday.
"In a way, yes, it does complicate it (his defense). Mr Penn should be called to testify to respond about the stupidities he has said," Badillo added.
He said that based on years of working Guzman, he was certain he would not make such a self-incriminating statement. "He (Guzman) could not have made these claims... Mr Guzman is a very serious man, very intelligent," Badillo said.
"Where's the proof? Where's the audio?"
Neither Penn's publicist nor Rolling Stone replied to requests for comment on Wednesday.
In the article, Penn said he was not allowed to record his in-person conversation with Guzman. The Mexican fugitive later sent Penn a 17-minute video of answers after security issues stymied plans to hold a follow-up interview in person, and it does not contain the reported comments.
Penn, who met Guzman along with Mexican actress Kate del Castillo, wrote that Guzman proudly volunteered information on his illegal activities.
"I supply more heroin, methamphetamine, cocaine and marijuana than anybody else in the world. I have a fleet of submarines, airplanes, trucks and boats," Penn quoted Guzman as saying.
A government spokesman said on Tuesday that Mexico was not directly investigating Penn or del Castillo but rather the circumstances around the meeting.
Instant messages among Guzman, one of his lawyers and del Castillo published by local paper Milenio on Wednesday show that the kingpin initially had no idea who Penn was. They also show Guzman and del Castillo flirting.
BID TO AVOID SOLITARY CONFINEMENT
Badillo said he was poised to file a legal challenge on behalf of Guzman, whom he has represented since 1993, against his being held in isolation. He rejected the government's assertion that Guzman was being moved regularly from cell to cell as a security precaution.
The legal challenge is not a new tactic for Guzman's lawyers. Badillo filed seven previously during Guzman's incarceration and after his escape.
Badillo successfully filed a challenge while Guzman was on the run seeking to bar security forces from killing him as they sought to capture him.
He declined to elaborate on his wider legal defense strategy, which is aimed at avoiding Guzman's extradition to the United States, where he is wanted on an array of charges.
Mexican daily Milenio late on Tuesday published alleged private messages between del Castillo and Guzman. Badillo said he believed reports about them having a close relationship were "pure speculation."
Badillo said he saw no conflict in accepting payment for legal services from a wanted drug trafficker, saying all Mexican's have a right to a defense in court. He declined to say how much Guzman pays him.
