Embattled Commonwealth Games officials conceded a "major communication blunder" was to blame for Thursday's athletics farce as they continue to grapple with snags at the halfway point of the Delhi event on Friday.

-Commonwealth Games coverage

After a tumultuous build-up, the spectacular October 3 opening ceremony provided some brief respite before organisational nightmares returned to haunt the multi-sport gathering.

Australian Sally Pearson had completed her 100 metres victory lap on Thursday and was set to collect her gold medal when she was told about her disqualification some three hours after crossing the line.

"It was a major communication blunder," a visibly annoyed Commonwealth Games Federation (CGF) President Michael Fennell told a news conference on Friday.

"We received complaints how the athletes were held up before the medal ceremony, ... treatment of the athletes are unsatisfactory and we have alerted all the other sports as well to ensure that a similar incident does not occur.

"The athletes were waiting and didn't know there was a protest," he added.

A scoreboard collapsed at the rugby venue, swimmers complained about the water quality in the pool, while English and Australian athletes battled "Delhi Belly" at the Games Village.

Those lucky enough to elude the stomach bug have performed largely in front of empty galleries.

Organisers are also scampering to get special permission that would allow helicopters to fly over some of the city's restricted areas to cover cycling road race and marathon events.

Fennell put the last-minute scramble down to the organisers' "inexperience" and said there was no Plan B if the request was turned down.

"Many cities have restricted areas, what is normally done is you get a waiver for the event ... I'm pretty confident it should be obtained later in the day as everyone understands its importance.

"It should have been done before but there was not a clear understanding ... it could be put down to inexperience in terms of hosting events like this," Fennell said.

A barrier malfunction that left three Ugandan officials injured has further increased the organisers' embarrassment.

Games secretary general Lalit Bhanot said that Suresh Kalmadi, organising committee chairman, has written a letter to Uganda's high commissioner and the chef de mission apologising for the incident.

A local newspaper suggested one reason for the obvious gap between organisers' claims of sold-out events and the reality of sparse crowds. The Hindustan Times reported how a sackful of tickets found a way to a junk-dealer.

The prevailing chaos is in tune with the poor build-up of India's $6 billion exercise that was intended to rival China's near-flawless staging of the 2008 Olympic Games and underline the country's growing financial might.

"We are fully competent and everything is being resolved," Bhanot said.