The injury-prone 21-year-old walked laps during Tuesday's session at La Trobe University and will remain behind when his team travels to Perth later in the week.
Coach Matthew Knights said the injury was not serious and stemmed from an innocuous incident.
"He slightly twisted and locked up his back", said Knights. "However, Jason Winderlich copped a heavy knock last season, had a back spasm, then three or four days later freed up pretty well.
"We're hoping it's along similar lines to that. [Winderlich] came back and played pretty well for the rest of the season."
The setback is a frustration for Gumbleton, particularly after impressing with two goals in the Bombers' intra-club match in Shepparton last Wednesday.
He has missed the past two seasons with a range of injuries, including a back problem that required surgery in April last year.
But his coach said the young forward was already showing signs of improvement, and was walked with greater freedom on Tuesday.
"He's got a smile on his face this morning so we're aiming at that second round," Knights said.
Midfielder Brent Stanton will also miss the clash in Perth after having what Knights referred to as "interruption".
David Myers (hamstring) should play in the club's second NAB Cup match, and ruckman David Hille (knee) could yet score a match in the latter stages of the pre-season competition.
"If [Hille] is going to play round one, he's going to need some serious hit-outs before round one," Knights said.
"We're looking to later in the NAB Cup campaign and all tracks are leading to round one, pending that everything goes smoothly."
Hille, who ruptured his anterior cruciate ligament in round five last year, has been participating in all of the Bombers' contested drills and recently stepped up his ruck work.
Highly-rated key position prospect Michael Hurley has overcome his wrist injury but could still miss this Friday's game with the club yet to decide on a sanction for his post-season indiscretion.
The 19-year-old is facing five criminal charges that stem from an alleged assault on a taxi driver in September last year. His case was adjourned last month until March 5.
The leadership group will meet with the club's administration within the next 48 hours to decide on a course of action.
Draftee Jake Melksham, second-year forward Michael Still and former Hawthorn forward Mark Williams will all make their Essendon debuts against the Eagles.
Scott Gumbleton is a $94,500 forward in this year’s Toyota AFL Dream Team.
