Scotland international Martin, 28, has been on loan at Fulham this season, but in December indicated a desire to return to the Rams.
"I spoke to Chris. The general feeling is he wants to come back," Rowett told BBC Radio Derby.
"He's contracted to the club, he's coming back. He's a player I think the team has missed."
Martin was allowed to leave Derby last summer by then manager Nigel Pearson and has gone on to score 11 goals in 31 appearances for Fulham.
However, after Steve McClaren returned as Rams boss, Martin tried to cut short his loan deal, only for Fulham to refuse - and in a further twist to the saga, he signed a new contract at Pride Park in January.
Speaking on BBC Radio Derby's Sportscene programme, Rowett said: "At this moment in time, Chris Martin is our player and I fully expect him to be here next season."
Rowett, who has taken charge of seven games since succeeding McClaren last month, reassured supporters he had been given free rein by chairman Mel Morris to reshape the team - but warned there would be no lavish spending.
"I've got carte blanche to change whatever I need to change," Rowett said.
"I think we can get one or two in potentially, before we get some out.
"But when you've spent a lot of money on a lot of players and it hasn't quite borne the fruit of promotion then you're going to have to be a little bit more sensible.
"We're going to have to reduce what we're doing a tiny bit but I don't think that's going to affect the type of player that we can bring in."
In a wide-ranging phone-in with supporters, Rowett also spoke of the frustration at being without long-term injury victims Craig Forsyth and George Thorne.
Defender Forsyth ruptured his anterior cruciate ligament in August after missing the majority of last season with the same injury, while midfielder Thorne suffered a double leg break last May.
"They are hopefully on the mend and coming back," Rowett, 43, said.
"Craig Forsyth has been involved in training and done really well but George is a little bit further behind.
"They're both really committed to getting back and if we can have both of them fit for the start of next season then straight away the team looks to have a stronger, more powerful and more technical edge to it."
Derby County manager Gary Rowett says striker Chris Martin remains a big part of his future plans.