"I think it's pretty clear that this is a contract situation, which we've talked about internally," Flores told reporters Tuesday in a Zoom video conference.
"That's what I believe it is and obviously we've had discussions and we'll continue to have those discussions."
Howard can be fined more than $93,000 if he misses additional minicamp practices Wednesday and Thursday. The two-time Pro Bowl selection and 2020 All-Pro led the NFL with 20 passes defensed and 10 interceptions in 16 starts last season.
Howard is the latest star player to become a minicamp holdouts. New England Patriots cornerback Stephon Gilmore and Green Bay Packers quarterback Aaron Rodgers also skipped their team's mandatory practices this week.
The Dolphins signed Howard to a five-year, $75.2 million contract extension in 2019, which at the time made him the highest-paid cornerback in the NFL. His current pact runs through 2024.
Los Angeles Rams All-Pro Jalen Ramsey is the highest-paid cornerback in the league, with an average salary of $20 million per season. Howard's current pact features average annual salaries of $15 million, which ranks sixth in the NFL.
Howard's teammate, cornerback Byron Jones, makes an average of $16.5 million per season.
"It's very unique," Flores said of Howard's contract situation. "It's a renegotiation of an extension after one year, and it's honestly something that hasn't been done before.
"I'm not saying that we're drawing a line in the sand, but different players set the market every year. We love 'X.' ... He's very productive. He's a team player. He's an important player on this team; but again, it's a unique situation. We want to keep him here."
The Dolphins will return to Davie for training camp in late July.