Brown was a shadow of his box-to-box self in the 2-1 Champions League defeat by Benfica before being hooked by Lennon in the second half with Broony's inability to train full out clearly leaving him off the pace.
The Celtic manager also has injury concerns over Joe Ledley and Charlie Mulgrew, who may miss this weekend's visit of Inverness and James Forrest.
Lennon admitted: "We may have to wait on Scott, the problem is in the stomach, hip pelvis area and it seems to flare up every now and again.
"But that wasn't the problem on Tuesday, he was cramping up because of his lack of training because he's been resting between games.
"We'll assess him and Joe Ledley is starting to show similar symptoms as Scott so we'll have to be careful with that.
"Charlie Mulgrew wasn't feeling very well at half-time and he may miss the Inverness game."
Forrest, who hasn't played since the 2-0 defeat by Kilmarnock last month, is rated at just 50-50 for the Champions League Parkhead finale with Spartak Moscow.
Lennon told Celtic TV: "James had a scan on Monday and it's come through that he has a tendon problem in the hamstring area.
"We're assessing that, but there always seems to be complications with James, the injuries he gets don't seem to be straightforward. We're hoping, and it's an outside chance, that he'll be fit for Spartak Moscow."
Meanwhile, Hoops hero Efe Ambrose says he's going to use taming Lionel Messi as the inspiration for getting the Hoops through to the Champions League last 16.
Celtic will qualify for the knockout stages of the tournament if they can better Benfica's score on the final game of the groups next month.
And the Nigerian reckons keeping Barca legend Messi quiet in their famous 2-1 win proves Celtic are good enough to mix it with the big boys in the next stage.
Ambrose said: "Messi is a good player and nobody will argue against that, but in that match we made things difficult for him and he will never forget playing against a team like Celtic.
"That is the spirit we will be taking to the last game to make sure that we win – though the result from the other game will determine our fate.
"But we are going to do our best to ensure that we make it through. I strongly believe that we are going to make it, we started well and we want to finish the good work.
"Our last game is back in Scotland and we will be back on our ground and we need to win. It was a great achievement to beat Barcelona and I can never forget that game.
"But in the whole of the Champions League, we are looking beyond just beating Barcelona – we want to go far in the competition."