The 18-year-old fan-favourite hasn't featured since January 11, after previously impressing in the Saddlers midfield.
Fans have questioned his absence from the team in recent weeks but Clarke has insisted Bates is firmly in his first-team thoughts.
"People on the outside might have it on their agendas that he's out in the cold, but it's a load of rubbish," he said.
"Alfie Bates is an 18-year-old kid that has done absolutely fantastic so far this season.
"His performances recently have been inconsistent, in his own words, and we'll keep working away with the lad, that's football.
"I have a tremendous group with a tremendous work ethic– they have a fantastic spirit.
"We're all together here and Alfie is one of the young lads that are trying to break through into the first team on a regular basis.
"He's a great kid with a great attitude and hopefully he has a good career in the game."
Bates fell further down the pecking order after the introduction of on-loan midfielder Nathan Sheron.
The 22-year-old has since hailed his new manager as 'brilliant' as his new team-mates made him welcome in the Black Country.
"He's (Darrell Clarke) been brilliant," he said.
"All of the staff and all of the players have been brilliant with me.
"I couldn't ask for a better welcome."
Sheron, who joined until the end of the season from League One Fleetwood, has started all three games since his arrival, playing 90 minutes in two of them.
The utility man, who can also play across the defence, is aiming for a successful end to the season for Walsall.
"We want a good end to the season – we're an ambitious club so we'll try and get better, taking it game by game," he added.
"I'm just here to try and help the team out and to try and get results.
"We want to push on.
"Competition is a good thing, it drives you and makes you want to get the best every week.
"They care a lot about the games and Darrell's a really good manager."