The troubled Commonwealth Games in Delhi have been hit by a new problem: thousands of condoms blocking drains at the £150m athletes' village.

Games organisers have said they will work round the clock to clear the prophylactics from pipes at the accommodation blocks housing more than 7,000 athletes and officials.

Mike Fennell, president of the Commonwealth Games Federation, sought to put a positive spin on the story at a news conference, saying: "If that is happening, it shows that there is use of condoms and I think that is a very positive story. Athletes are being responsible."

"If they are so active then that's very good," a spokesperson for the organisers said. "We are promoting safe sex."

One official told the local Mail Today newspaper, which broke the story, that more than 4,000 condoms had already been taken from free vending machines since athletes started arriving 10 days ago.

The condom blockage follows an outbreak of gastrocolic problems such as diarrhoea among swimmers this week. Fennell said an urgent inquiry had been ordered into whether contaminated water at the event's newly refurbished swimming pool was responsible for 15 Australian and English swimmers becoming sick.

"If there is something that is unsafe, you can't swim in that water. It's a matter we have to deal with with the greatest of urgency," said Fennell, who has been criticised for his handling of the chaotic runup to the games.

The Indian organisers have insisted that water in both the main pool and the warm-up pool at the aquatic complex was tested, with nothing untoward found. "We don't know why they have fallen ill but it is not the water. Not all the swimmers have fallen sick. Maybe this group went out to eat something somewhere," a spokeswoman said.

A spokesman for Australia's swimming team, Lachlan Searle, said "about a half-dozen" swimmers had been affected by stomach problems. At least three Australians are thought to have gastroenteritis.

Caroline Searle, the England team spokeswoman, said fewer than one in 10 of England's 541 athletes had been affected by a "mild 24-hour stomach condition" since arriving in Delhi.

"Not everybody all in one sport has been ill. There are little pockets across all sports. The levels of mild 24-hour stomach conditions are in fact lower than we anticipated," she said. "We are not complacent as they may well rise in coming days but no athlete has so far been forced to miss any session through illness."

The England hockey team has been affected.

Crowds have continued to be thin at most of the venues but Suresh Kalmadi, chairman of the local organising committee, said 125,000 tickets had been sold in recent days, promising full stands in coming days. Earlier in the week he suggested free tickets might be distributed to school children or the poor to fill seats.

The chaotic Indian preparations for the 19th Commonwealth Games sparked talk of a boycott of the event, which is thought to have cost between £3bn-£6bn to stage. Sunday's opening ceremony briefly allayed the criticism but a series of transport issues, technical malfunctions and problems with food have fuelled further negative coverage.

Distributing thousands of free condoms to athletes has been a tradition since the 1992 Barcelona Olympics. At the Sydney Olympics in 2000 athletes quickly used up the 70,000 free condomsprophylactics, forcing organisers to supply another 20,000, while in Athens four years later the provision was doubled to 130,000. At both the Beijing Games in 2008 and the Vancouver winter Olympics in February 100,000 condoms were provided.