The fine is for failing to interview minority candidates in his search for a head coach last winter before he hired Steve Mariucci away from San Francisco.
The league said Millen was part of a commitment to endorse a recommendation by the NFL's Diversity Committee.
In a letter, Commissioner Paul Tagliabue told Millen that he reneged on his commitment to the agreed-upon process.
In a statement, the Lions expressed disappointment.
"While we respectfully disagree with the decision made by the Commissioner and the League's Diversity Committee, .. we remain proud of the Lions' long-standing record of diversity within our employment ranks," said team spokesman Bill Keenist. "We will have no other comments on this issue, choosing rather to focus on the start of training camp and the 2003 football season."
Previously, he told teams that future breaches for the head coach position will be subject to fines of $500,000 or higher as "conduct detrimental" to the NFL.