Lee, 22, played five times at the World Cup after recovering from a long-term Achilles tendon injury but has made just one regional appearance since.
"He's not ready," head coach Wayne Pivac told BBC Wales Sport.
"We just want to get him to a space for us where we think he needs to be."
Pete Edwards, 35, is likely to continue to deputise for Lee with another Wales international, Rhodri Jones, still several weeks away from fitness.
Canada wing DTH van der Merwe will return after a fortnight's rest, while fly-half Steve Shingler is expected to be fit after a toe injury.
Full-back Aled Thomas, who suffered a head knock in the Scarlets' previous game against Leinster, is also likely to recover.
On the omission of Lee, Pivac added: "This is a decision we've made.
"We want to get Samson into the best place possible for both the region and Wales going forward. His future is important to everybody.
"Peter Edwards did a very good job against Munster when he came on (for Lee), we're happy with Pete but we desperately want to get Samson back into shape as quickly as possible so we can share that workload."
Edwards, known as 'Pete the Meat', returned to Scarlets last year after a spell with London Welsh.
"When given the opportunity I felt I took it and it's just carried on really," said Edwards.
"I've always previously just been a squad boy and played when there are injuries, so playing against boys who you've watched as internationals is a bit weird."
Edwards blames former team-mate Rob McCusker for his nickname.
"When we first met, he put me down as 'all you can eat' in his phone and when his wife asked who was ringing, he said 'all you can eat, Pete the Meat'," he said.
"It comes off the tongue, so that's how it came about."
Scarlets will leave out Wales tight-head prop Samson Lee for their European Champions Cup opener against Northampton amid concerns about his general fitness.