Barts Health NHS Trust was placed in special measures in March, but has faced further inspections by the Care Quality Commission.
It said "too little attention" was paid to safety and pointed out leadership failings at the organisation.
The trust said it was "very sorry" and that it was facing a "big challenge".
Barts Health NHS Trust is responsible for the care of around 2.5 million people.
It was placed into special measures when a culture of bullying and low morale was discovered among staff at one of the hospitals it runs, Whipps Cross in Leytonstone, east London.
Fresh concerns have now been raised at the Royal London Hospital and Newham University Hospital.
The CQC said patient safety was not given sufficient priority, staff were discouraged from raising their concerns amid a culture of blame.
It added that staffing was significantly below recommended levels and the hospitals were so full that patients were not always cared for on appropriate wards.
Some faced delays of more than 18 weeks from referral to treatment and some patients had their surgery cancelled on several occasions due to a lack of beds.
Prof Sir Mike Richards, the chief inspector of hospitals, said: "It is clear that the leadership issues we found at Whipps Cross were replicated at the other hospitals.
"There is still a lack of engagement with the staff, low morale, high levels of stress, even confusion among the workforce about who is in charge.
"Across the trust there is too little attention paid to safety, with failures in incident reporting and auditing, and in dealing with or learning from complaints.
"If the trust is to turn round then it must focus first on the culture and on the leadership issues so that it can effectively deal with all the individual concerns which we have identified on this inspection."
The CQC has identified 65 areas where the trust must make improvements.
Steve Ryan, the chief medical officer at Barts Health NHS Trust, said: "We are very sorry for the failings identified by the CQC in some of our services at Newham and the Royal London hospitals.
"We know we have a big challenge ahead but we are determined to rise to that challenge.
"We are already making rapid and dramatic improvements in key areas. We welcome the targeted help the special measures regime provides to support our improvement journey.  All our hospitals will be part of the trust's improvement plan in response to special measures, ensuring a consistent approach to the provision and delivery of high quality care.  We will work with each of our hospitals with the same level of urgency and commitment."
Services run by the biggest NHS trust, including two more of its hospitals, have been labelled "inadequate" by inspectors.