He said: "I don't think there is any evidence that across the whole range of services in these hospitals there are major failings that should worry the public.
"But there are undoubtedly pockets of poor performance and those have got to be dealt with."
Monitor announced on Friday that Richard Borne had been relieved of his post at the Colchester trust, citing poor leadership.
It said the trust, which had been under review for nine months, had failed to meet waiting targets for A&E and cancer care, or to provide acceptable standards of patient care.
Death rates among patients were also 12% higher than expected.
Sir William said: "For the last six months we have been meeting Colchester with increasing frequency, and we have been pointing out to them the whole range of aspects of care and quality of service that are not up to scratch.
"The conclusion we have reached is that under the present leadership the board is simply not tackling these issues fast enough or thoroughly enough to put them right."
Mr Bourne, who is seeking legal advice over the loss of his job at Colchester, said he was "shocked" by the decision.
The announcement comes less than 24 hours after the regulator highlighted major lapses in hygiene and unusually high death rates at the Basildon and Thurrock NHS Trust.
A taskforce has been sent in to force through improvements.
These reports are a tragedy for patients, their families, and for staff working at the hospital
Baroness Young, chair of the Care Quality Commission (CQC), which is responsible for inspecting all NHS trusts, admitted that the current inspection system - which the commission inherited from its predecessor - was flawed.
She said reforms - which would place a greater emphasis on the view of patients - would soon be in place.
The CQC rated the Basildon trust as "good" overall in October. But a new report from an unannounced inspection team carried out by the CQC found evidence of sub-standard care.
The inspectors saw:
• Floors and curtains stained with blood
• Blood splattered on trays used to carry equipment
• Badly soiled mattresses in the A&E department with stains soaked through to the foam filling
• Items that should only be used once still in use
• Equipment in the resuscitation room that was past the use-by date
• A children's blood pressure cuff heavily stained with blood
• Suction machines contaminated with fluid inside and out, with what looked like mould growing on the equipment
The inspectors criticised a poor care environment in A&E, in particular a lack of privacy for patients.
They also highlighted inadequate arrangements to treat children, with few specialist paediatric staff.
Cynthia Bower, CQC chief executive, said swift action was needed to "nip problems in the bud".
She said: "Our work has uncovered serious failings. The trust has high mortality rates for emergency admissions and we have found evidence of significant problems in different parts of the organisation."
The Basildon trust said it had taken action to improve standards, such as employing more nurses and drawing up plans for a new casualty department.
Senior doctors at the trust also argued that death rates are not a serious problem.
Katherine Murphy, director of the Patients Association, said: "How many times do the public need to keep hearing about this before the government is embarrassed enough to do something about it?
"The system of regulation and supervision needs to be urgently reformed."
Public sector union Unison called for the Basildon trust to be taken back under NHS control, and for a public enquiry into patient care at the hospital.
Karen Jennings, the union's health specialist, said: "These reports are a tragedy for patients, their families, and for staff working at the hospital."
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