The Healthcare Commission's snapshot study last September looked at tests such as X-rays, scans and blood checks.
It warned some trusts might not meet the 2008 target that no-one should wait more than 18 weeks from GP referral to their first hospital treatment.
But the government said progress had been made in recent months and it was confident the target would be met.
In order to meet the 18-week target, the government has said all diagnostic tests must be carried out within 13 weeks by March 2007.
Figures released earlier this month showed that, at the end of June, patients needing a total of 191,370 diagnostic tests were still waiting more than 13 weeks.
The Healthcare Commission's report covers the 153 acute trusts in England. It looked at X-rays and scans, endoscopies (examinations of the bowel and stomach) and pathology (tests on blood and tissue samples).
There are more than 30m imaging examinations per year, and the 175m pathology requests inform 60% of medical decisions.
The report took into account he experiences of patients and clinical quality, as well as the efficiency and management of services.
Sixteen trusts were rated as "excellent", while 15 scored the lowest rating of "weak". Sixty-one trusts got a rating of "good" and 61 were "fair".
While overall waits for endoscopies were falling, a "postcode lottery" existed at some trusts, the commission found, with waits of between two weeks and more than a year.
Its report said: "In many trusts, waits are being reduced too slowly to meet the government's 18-week target or the likely surge in demand expected from full implementation of the new national bowel cancer screening programme."
And 45% of trusts could not provide data on the success rate for diagnosing problems as a result of endoscopies, despite the fact that at least 32,000 colonoscopies a year do not produce a successful diagnosis.
In addition, just 41% of trusts were achieving the 90% success target agreed as part of the bowel cancer programme.
When the commission looked at how quickly pathology tests were turned around - for example for a heart attack patient in A&E - 15% of trusts took more than two hours.
The results of the survey were given to trusts in March, so that action plans could be implemented to tackle long waits.
Anna Walker, chief executive of the Healthcare Commission, said: "This review highlights the excellent efforts being made by many trusts in reducing waiting times for scans.
"However it has also revealed great variations in trust performance, in many areas of diagnostics.
"Some patients are still waiting too long for diagnosis, delaying their treatment, and too many internal examinations fail to achieve a result, slowing down diagnosis and causing distress to patients.
Dr Gill Morgan, chief executive of the NHS Confederation which represents over 90% of NHS organisations, said: "There have been overall improvements but it is clear that problems remain.
"There has been significant investment in making new providers available to help with this problem but it needs skilled management to ensure that results of diagnostic tests and scans are made available to individual NHS trusts."
Public health minister Caroline Flint said improving diagnostic testing was a key priority for the government.
She added: "The Healthcare Commission acknowledges that there have already been significant improvements in overall waiting times for scans, even against a backdrop of increasing demand.
"We are confident the NHS will deliver the 18-week target."