The Hearts manager was responding to an article in yesterday's Scotsman in which a source said that the midfielder was upset by the way in which he had been relieved of the captaincy, calling it disrespectful, and implying that Stewart would not turn out for the club again.
The player had to train with the youth squad yesterday, although Jefferies said he had not yet decided on his squad for tomorrow's league game against Hibernian. The manager spoke diplomatically about Stewart, who is out of contract at the end of the season, making it clear there had been no ruling against including him in the team for the three remaining matches.
"Nobody from the club has said he's played his last game," the manager said yesterday. "He hasn't made me aware that he's played his last game. I haven't decided the squad yet. What I do will have nothing to do with the captaincy article, I'll assure you of that. I'll pick the squad based on what I think is the right squad for Hibs, based on how I want to set up and how we're going to play. I'll do that after training today.
"I'll take a squad away and I'll have a look at things I am not sure about, and have a look at other people playing in a position I've got a problem with. And we will see what materialises."
Jefferies confirmed, however, that Marius Zaliukas would continue as captain in place of Stewart. The centre-half, appointed deputy skipper to Stewart by former manager Csaba Laszlo, took over the armband when the midfielder was injured, but has retained it in recent games even when Stewart has been in the team.
The manager restated his belief that he should not be bound by decisions made by one of his predecessors, and said it made sense to keep Zaliukas as captain. "As far as the captaincy goes, he (Stewart] had trained all week but Marius had been playing.
"If I want to think about somebody else for captain next year – and we'll have to if Michael isn't going to be here – then is there anything wrong in just having a look at Marius as a contender?
"He's going to be here, unless a really big offer comes in. As far as contracts go he's here. And I can tell you this, I've already spoken to Marius. I changed my mind, because we're still in with a chance, but I said that, before the end of the season, I might give somebody else a shot.
"I don't think there's anything wrong with that. I don't think anybody should be too over- dramatic when they consider that, if there's a possibility he's not going to be here, I'm looking at other options.
"If things are tight and we're still in with a chance of Europe, I'll not just throw it to someone else at the moment. I'll tell Marius to continue. If it doesn't go our way in the last couple of games, you might find another two captains being named."
Jefferies implied he had gone out of his way to give Stewart a chance in recent weeks since the player recovered from a thigh strain. "He had trained for two days and then I put him in the squad for Ibrox. He got on when I could have chosen others before him.
"On Saturday (when Hearts lost to Motherwell] I left out Laryea Kingston and Ian Black, who had done well for us, to play him. And the last thing I said to him before we went out was that he has trained great this week. I told him that's why he had got the nod ahead of two boys that had done well.
"I told him just to concentrate on the football side and leave Marius to take the armband. I was thinking of next year and I think someone is making an issue of something that is not a problem."