However, Thomas Cook said the results did not explain the sudden deaths of its two guests, travel agent Susan Cooper and her husband John, at the Steigenberger Aqua Magic Hotel.
Thomas Cook commissioned an independent hygiene specialist and air quality specialist to conduct the tests, which covered food, water and air. They included tests on the swimming pool, carbon monoxide and carbon dioxide levels, air conditioning units and an audit of food storage, preparations and equipment.
But they were denied access to the Cooper's hotel room, where husband and wife were found dying on August 21, as this has remained under the control of the Egyptian authorities due to their ongoing investigation, said Cook.
The examination of air and water quality throughout the rest of the hotel was clear, there was no evidence of carbon monoxide and there were normal carbon dioxide levels in the vicinity of the room.
The tests on the swimming pools showed normal levels of chlorine.
The tests on the food and hygiene standards identified a high level of e-coli and staphylococcus bacteria, but no shigella, listeria or salmonella.
The preliminary results have been reviewed by an independent expert,Doctor Vanya Gant, the consultant and divisional dlinical director in microbiology and infection at University College London Hospitals NHS Foundation Trust.
"We have also shared these findings with the Cooper family, the Egyptian authorities and the Deutsche Hospitality group which has a franchise agreement with the Steigenberger Aqua Magic Hotel," said Thomas Cook in a statement.
It added: "It is clear from these results that something went wrong in August at the Steigenberger Aqua Magic Hotel in Hurghada and that standards fell below what we expect from our hotel partners.
"This is also supported by a review that we have conducted of our customer satisfaction scores, which fell sharply during this month. It is likely that the presence of e-coli and staphylococcus would explain the raised level of illness reported among guests at the hotel during this time, supporting Thomas Cook's decision to remove our 300 customers.
"However, neither our independent specialists nor Doctor Vanya Gant believe that these results shed any light on the still unexplained cause of death of Mr and Mrs Cooper. We await the results of the autopsies being conducted by the Egyptian authorities."
Thomas Cook said it has now decided to roll out a programme of specialist hygiene assessments to all hotels which experience a higher than average reported level of sickness.
All customers who told the operator they were ill during their stay at the Steigenberger Aqua Magic Hotel during August will receive compensation, said the operator.
"We are aware of 14 other customers who have reported sickness directly to us," said a spokeswoman.
"We take all reports of sickness seriously and we are very sorry for any customers whose holidays have been spoiled by illness. We have already put in place a dedicated team to prioritise all complaints from this hotel," it added.
The Steigenberger Aqua Magic Hotel remains on stop sale to Thomas Cook customers until further notice.
Thomas Cook chief executive Peter Fankhauser said: "Everyone at Thomas Cook is deeply saddened by the tragic deaths of John and Susan Cooper while staying at the Steigenberger Aqua Magic Hotel in Hurghada. Susan was a longstanding and much-loved colleague of ours.
"We continue to await the results of the investigation being conducted by the Egyptian authorities and are working closely with the Foreign and Commonwealth Office to ensure we prioritise the very best interests of the Cooper family.
"However, the tests that Thomas Cook commissioned and announced today show that hygiene at the Steigenberger Aqua Magic Hotel during the month of August did not meet the standards we expect. I am very sorry for all our customers who fell ill while on a Thomas Cook holiday at this hotel.
"These results, while not establishing the cause of the tragic deaths of John and Susan Cooper, have prompted us to commit further resource to tackle hygiene standards in those hotels where we identify a higher than average level of sickness.
"At any one time, Thomas Cook has more than 500,000 people holidaying with us somewhere in the world. We will continue to do all that we can to keep them safe and well on what should be the happiest weeks of their year."
A spokeswoman said the operator was working out at the moment how many hotels would require a specialist hygiene assessment. When asked why this wasn't already routine, she said: "We commission independent auditors SGS to audit all 3000 of our core properties yearly, to standards that in many cases are higher than those elsewhere in the industry. These audits are broad and cover a range of aspects surrounding the accommodation."
Courtesy of Travelmole
Independent testing carried out at the hotel in Hurghada where a British couple died last month have revealed a high level of e-coli and staphylococcus bacteria, which can cause food poisoning.