The 28-year-old irked the national team boss when he withdrew from the squad for last November's World Cup qualifiers against Moldova and Denmark but was subsequently pictured training with his club.
After leaving him out for the upcoming matches against Poland and then either Wales or Austria, Clarke revealed on Monday that Fraser had apologised to him.
Howe is confident the situation will soon be resolved amicably and the Newcastle attacker, who has been in fine form recently at club level, will work his way back into the squad.
"I've spoken with Steve and I've got a good relationship with him and I know how highly he rates Ryan, so I'm sure that situation will come to a positive conclusion," said Howe.
"The only thing I'll say on that is that it will be dependent on how Ryan performs, that will be the biggest factor in whether things change.
"He's very passionate about his country. He always has been from the first meetings I had with him. He loves his country.
"He was playing, when we first signed him [at Bournemouth], for the junior age groups and always loved going away, and that's not changed for Ryan. He wants to do well in every aspect for his football club and country.
"I'm disappointed for him, of course, but I think Ryan is in a good place because he's here, he's playing and he's playing very well."
Fraser came on as a late substitute against Chelsea last weekend, but prior to that was a regular starter in a resurgent Newcastle side.
"He had a slight tight hamstring before Chelsea, so we didn't want to risk him unduly in the game, but we're very, very pleased with his recent performances and I know, if he continues with the consistency of what he's delivering, then he'll force is way into that (Scotland) squad," said Howe.
Clarke had said on Monday that he is open to Fraser returning if he continues to deliver for Newcastle.
“We've agreed that Ryan's club form will determine whether he's involved in the next camps," he explained.