The Championship's leading scorer dislocated his troublesome right shoulder during the win over Ipswich and is seeing a specialist to assess the damage.
Latics are hoping the Duke will get the green light to continue playing as he is bang in form at the moment with five goals in his last five games.
The injury stems back more than two years and forced him to undergo surgery at the end of the Second Division title campaign.
It flared up again earlier this season and Ellington has attempted to keep it under control by strengthening the shoulder with a weights programme in the gym.
Manager Paul Jewell said: "The Duke took a knock in the last minute against Ipswich and the shoulder popped out.
"It went back in, he was fine over the weekend, and then it came out again when he rolled over in bed – something as simple as that.
"He's seeing the specialist but we hope that with a bit of tender, loving care and by telling him how good he is, he'll be okay for Saturday!
"Nathan has been wearing a harness to protect the shoulder in some games and has been doing strengthening exercises.
"But he was ill last week and couldn't get into the gym, and maybe that has played a little part in what has happened."
Jewell seems fairly confident that the 22-goal striker will be available to shoot down Millwall and continue his successful forward partnership with Jason Roberts.
That partnership and their friendship off the pitch was questioned by a couple of national newspapers earlier this week in the wake of an incident during the Ipswich game.
Ellington chose to shoot rather than pass to his better positioned colleague, earning himself a public flea in the ear from Roberts.
That fuelled talk of a rift between the pair, but the rumour has been angrily denied by Jewell.
He said: "What we saw on Saturday happens with strikers all the time.
"Nathan and Jason are best of friends off the pitch and I was disappointed to be made aware of the reports.
"It's a complete fabrication, and to suggest it could stop us getting promotion is total nonsense.
"Jason was disappointed the Duke didn't pass on Saturday because it would have been a certain goal.
"I thought Nathan should have passed, but he didn't. That's life, so let's not make a big issue out of it.
"We are top of the league at the moment, if people want to talk about silly factors like this, I'm not going to get involved.
"At Bradford I played with arguably the greediest striker in the world, Sean McCarthy, and while we were best of mates off the pitch, on it he was a nightmare!"
Meanwhile, Jewell has admitted encountering some difficulties in his latest attempt to strengthen the Latics squad.
He is believed to be chasing Reading striker Nicky Forster as he seeks cover for the front two, with a £150,000 offer having been made.
Jewell said: "We have made contact with a club and spoken to the agent involved, but in transfers you find that the goalposts move from day to day.
"There's more of a problem now than there was a couple of days ago, and if it doesn't come off we will move on to someone else."
Forster, 31, is believed to be keen to see out the remaining few months of his contract at Reading as that triggers a loyalty bonus, while an injury to Les Ferdinand could see win his first team place there.
Latics are hoping the Duke will get the green light to continue playing as he is bang in form at the moment with five goals in his last five games.
The injury stems back more than two years and forced him to undergo surgery at the end of the Second Division title campaign.
It flared up again earlier this season and Ellington has attempted to keep it under control by strengthening the shoulder with a weights programme in the gym.
Manager Paul Jewell said: "The Duke took a knock in the last minute against Ipswich and the shoulder popped out.
"It went back in, he was fine over the weekend, and then it came out again when he rolled over in bed – something as simple as that.
"He's seeing the specialist but we hope that with a bit of tender, loving care and by telling him how good he is, he'll be okay for Saturday!
"Nathan has been wearing a harness to protect the shoulder in some games and has been doing strengthening exercises.
"But he was ill last week and couldn't get into the gym, and maybe that has played a little part in what has happened."
Jewell seems fairly confident that the 22-goal striker will be available to shoot down Millwall and continue his successful forward partnership with Jason Roberts.
That partnership and their friendship off the pitch was questioned by a couple of national newspapers earlier this week in the wake of an incident during the Ipswich game.
Ellington chose to shoot rather than pass to his better positioned colleague, earning himself a public flea in the ear from Roberts.
That fuelled talk of a rift between the pair, but the rumour has been angrily denied by Jewell.
He said: "What we saw on Saturday happens with strikers all the time.
"Nathan and Jason are best of friends off the pitch and I was disappointed to be made aware of the reports.
"It's a complete fabrication, and to suggest it could stop us getting promotion is total nonsense.
"Jason was disappointed the Duke didn't pass on Saturday because it would have been a certain goal.
"I thought Nathan should have passed, but he didn't. That's life, so let's not make a big issue out of it.
"We are top of the league at the moment, if people want to talk about silly factors like this, I'm not going to get involved.
"At Bradford I played with arguably the greediest striker in the world, Sean McCarthy, and while we were best of mates off the pitch, on it he was a nightmare!"
Meanwhile, Jewell has admitted encountering some difficulties in his latest attempt to strengthen the Latics squad.
He is believed to be chasing Reading striker Nicky Forster as he seeks cover for the front two, with a £150,000 offer having been made.
Jewell said: "We have made contact with a club and spoken to the agent involved, but in transfers you find that the goalposts move from day to day.
"There's more of a problem now than there was a couple of days ago, and if it doesn't come off we will move on to someone else."
Forster, 31, is believed to be keen to see out the remaining few months of his contract at Reading as that triggers a loyalty bonus, while an injury to Les Ferdinand could see win his first team place there.