The Official UK Charts Company says it is "pleased" with the first singles chart to include legal downloads.
Damon Albarn's Gorillaz entered the revamped chart at 22
But a spokesman said there would be "a certain amount of fluidity" in chart rules in the weeks and months ahead.
The inclusion of digital sales has almost doubled the singles market, with 383,000 downloads sold last week compared with 393,000 physical singles.
The British Phonographic Industry (BPI) has welcomed the chart as "an historic day for the UK music industry".
"The addition of downloads to the singles chart doubles the market at a stroke," said BPI chairman Peter Jamieson.
"By bringing new people back into the singles market, the addition of downloads by definition makes it more representative."
However, the Association of Independent Music (AIM) said independent labels and artists have suffered under the new system.
AIM had tried to delay the chart changes, claiming independent labels found it hard to get music on major download services.
It has now taken its case to the Office of Fair Trading.
The Official Charts Company (OCC) said there was one more independent (or "indie") entry in the revamped Top 40 than in the physical sales chart.
"There are eight indie entries in the Top 40, compared to seven otherwise," said the company's spokesman.
But AIM said two thirds of indie singles in the Top 75 are lower than they would have been without combination.
One of them is Melanie C's Next Best Superstar, which enters the combined chart at 30. Without downloads the former Spice Girl would have come in at 25.
"The facts speak for themselves," said an AIM spokesman.
Fears that the chart could be fixed in some way appear to be unfounded, according to the OCC representative.
DOWNLOAD SERVICES TAKING PART INCLUDE
The Music Engine
Source: Official Charts Company
"We have total confidence in the systems we've put in place," he said. "People should feel confident the chart is free from unfair manipulation."
However, tactics used by Damon Albarn's cartoon dance act Gorillaz may lead to a rethink of the rules governing the chart.
Gorillaz released a limited edition of just 300 copies of their new single Feel Good Inc to shops.
The single charts at number 197 in the shop-only chart. But thanks to download sales the song entered the rundown at number 22 - a gain of 175 places.
"We've put some rules in place but we will revisit them on a regular basis," said the OCC spokesman.
"We don't say how many copies have to be available in the market place, but we would hope companies will act in the spirit of the chart rules."
Mel C is five places higher in the non-download chart
Seven singles in the Top 10 moved places due to the changes, but none moved more than one place up or down.
Tony Christie's hit (Is This The Way To) Amarillo was top in both the new combined chart and the old-style shop chart.
"The fact there is so much correlation between the two charts means the new chart reflects the most popular songs out there," said the OCC.
Plans are underway to launch an integrated album chart to reflect the rise in digital album sales.
The download services taking part are: Apple iTunes, Napster, MyCokeMusic, Woolworths, Virgin, HMV, Wippit, easyMusic, The Music Engine, Bleep7 Digital Media, MSN Music, Big Noise, Tiscali Music, Wanadoo, City16, Recordstore.co.uk and Karma Download.