The complaint filed Tuesday in New York calls Daniels' statements "egregious" and attempts to distance Penn's behavior from Howard's.
"Daniels falsely equates Penn with Howard, even though, while he has certainly had several brushes with the law, Penn (unlike Howard) has never been arrested, much less convicted, for domestic violence, as his ex-wives (including Madonna) would confirm and attest," the filing reads.
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Howard has been arrested for violence against women, according to various media reports and Penn's complaint. Penn has been accused of abusing pop star Madonna when they were married, according to multiple media reports.
The lawsuit goes to great lengths to describe Penn's contributions to society, calling him "one of this generation's most highly acclaimed and greatest artists and humanitarians." It also contends that Daniels "seems to condone Howard's reported misconduct" and suggests he used the interview to generate buzz around "Empire" before Sunday's Emmy Awards. "Empire" returns to TV for a second season this week.
Daniels' representatives did not immediately respond to CNBC's request to comment.
—CNBC's Jim Forkin contributed to this report.