The track, which is currently number one on iTunes, is available for free when pre-ordering his forthcoming album The Next Day. This would have prevented it from entering the chart.
However, the Official Charts Company has since said that sales of the single track do count towards the official Top 40, meaning 'Where Are We Now?' will enter if it achieves enough sales.
Their earlier statement read: "Owing to chart rules which are agreed in partnership with UK record companies and retailers, data relating to the David Bowie single 'Where Are We Now' cannot currently be counted towards the official singles charts, as the release is linked to an album pre-order promotion and it is not possible to distinguish album sales from track sales from the retail data received.
"Should it become possible in the future for regular track sales to be distinguished from album pre-order incentive purchases, then these sales can be counted towards the chart."
'Where Are We Now?' marks the singer's first new release in over a decade and shot to the top of the download chart less than a day after its surprise release yesterday.
Bowie has also seen a surge in sales of his hits collection The Best of Bowie since news of his upcoming studio LP was announced.
Lady GaGa recently praised 'Where Are We Now?' on her Twitter page, calling it "a moment of bliss".
Watch the 'Where Are We Now?' video below:
Photo gallery - Bowie through the years:
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