Appearing as a guest on Marlins flagship station 790 The Ticket's "Hot Stove Show" on Saturday, Hill was asked if Johnson would be with the team next season.
"Yes, I can say with certainty, yes," Hill said.
The Hot Stove Show debuted on Saturday from 2-4 p.m. ET, and the show is available online at Marlins.com.
Hosts Josh Friedman and Craig Mish addressed a number of topics in a lengthy interview with the Marlins' general manager.
Johnson's long-term future with the Marlins is in question because negotiations for a multiyear contract broke down earlier this month.
Matt Sosnick, the pitcher's agent, said recently both sides couldn't agree on the years or dollars. Johnson was seeking a four-year deal, with the Marlins offering three years with a club option.
"It's unfortunate that it did get out there, because that's not how we operate," Hill said. "But from the standpoint of Josh's future, and how he fits, and how attractive he looks, no matter what his situation is, he's a good player, and a good pitcher. I don't ever think there would be a shortage of teams that would want to have him on their team, and we're very fortunate to have him as a member of the Marlins."
Johnson is in his second year of arbitration, and he won't have the necessary service time to be eligible for free agency until after the 2011 season.
So, the Marlins have the leverage to sign their ace right-hander, who finished 15-5 with a 3.23 ERA, for two more seasons.
Many are speculating that because the Marlins were unable to reach agreement on a multiyear deal, Johnson may be moved either this year or next.
"Obviously, Josh Johnson is a big part of our club," Hill said on the radio show. "He is a second-time [arbitration-eligible] pitcher who we still have under control for two more years. From that standpoint, he's going to be here. The strength of this organization is built with our pitching."
Unless talks for a multiyear deal re-open, both sides are prepared to work out a one-year deal for 2010. The All-Star is expected to see his salary rise from $1.4 million in 2009 to about $4.2 million next year.
While Hill insisted that Johnson will be with Florida in 2010, he didn't indicate if the 6-foot-7 right-hander would be with the club in 2011.
The Marlins' options for Johnson the next couple of years are simple: Seek a trade before he becomes a free agent, or seek Draft-pick compensation in 2012 if he signs elsewhere as a free agent. Another possibility is to re-open talks in hopes of reaching a multiyear deal. At this point, that scenario seems unlikely.
"Josh is very talented and one of the better starting pitchers in the National League," Hill said.
As the Marlins prepare for the Winter Meetings, which begin Dec. 7 in Indianapolis, Ind., the team's objective is to build around pitching.
"Our philosophy is fairly straightforward," Hill said. "We feel that when we pitch, we give ourselves an opportunity to win a ballgame every night. We need five guys to step up and get us deep into ballgames and take pressure off our bullpen.
"From our standpoint, that's the most important thing for us moving to 2010, is making sure that our pitching, and our starting pitching, does what it's capable of doing."
As things stand now, Johnson promises to be a major part of the rotation.