The song, Where Are We Now?, created a buzz around the world on Tuesday when it appeared without warning and soon topped the download charts on iTunes.
But the Official Charts Company said sales of the song have not been counted towards this week's Top 40 because many sales are tied to orders for his new album.
Officials are now looking into whether the sales can be broken down further to allow it to be counted. If they can come to an agreement it may make the chart on Sunday after all.
Bowie ended his recording silence of almost 10 years by launching the single, with an album called The Next Day to follow in March.
Many fans had all but given up hope of him recording again after he largely withdrew from the public eye, with his last rare performances in 2006.
Where Are We Now? is still at number one in the iTunes chart and the forthcoming album is topping the download store's album chart on the strength of advance orders.
However, as well as sales in its own right, the single is also being given away to people who pre-order the full album. Chart chiefs say that, as it is not possible to differentiate, it cannot be counted for the singles chart.
A spokeswoman said: "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 be counted towards the official singles charts, as the release is linked to an album pre-order promotion."