An investigation by GP has found many patients wait months for tests such as colonoscopy.
It also revealed long delays in PCTs that did not expand diagnostics in 2011/12, despite extra DH funding.
Bowel Cancer UK warned that the DH cancer strategy 'will be compromised' if PCTs do not invest in endoscopy, and that PCTs need to prepare for 15% higher demand.
Prominent cancer GP and DH adviser Dr Nick Summerton said access to NHS endoscopy was now so poor that patients should be offered the chance to pay for faster tests.
The DH is giving PCTs £450m over four years from 2011/12 to improve early diagnosis of cancer. GPs were promised better access to diagnostic tests for their patients.
But data from 94 PCTs that responded to a Freedom of Information request show 50% of trusts made no attempt to expand or invest in additional endoscopy services in 2011/12.
The DH made investing in diagnostics and raising numbers of patients having scans a 'key priority' for the NHS in 2012/13.
But GP's investigation found 85% of PCTs that had not invested in 2011/12 had no plans to do so in 2012/13. Just 36% of trusts could explain how they plan to spend their share of the £450m on endoscopy in 2012/13.
By January, up to a quarter of patients in some PCTs that did not invest were waiting more than six weeks for colonoscopy. The figures cover patients who do not qualify for the two-week wait referral process.
From April, the DH expects less than 1% of patients to wait more than six weeks for a diagnostic test.
Latest figures for March show many trusts' waiting lists for colonoscopy have since improved.
But while the NHS now has just 0.7% of patients waiting this long across all type of diagnostic tests, one in 40 are waiting more than six weeks for colonoscopy or flexible sigmoidoscopy.
This means more than a thousand patients are waiting for these tests for longer than the DH target at any one time.
Data for March show many PCTs' waits for colonoscopy have since improved. But more than 1,000 patients are waiting longer than the DH target at any one time. This suggests dozens of areas will continue to breach this target when data for April are released.
Dr Summerton said colonoscopy services were 'saturated'.
Lack of capacity affects not just investigation of suspicious symptoms, he added, but also cancer screening and diagnosis for common benign conditions such as inflammatory bowel disease.
He said long waits were unfair and patients not eligible for two-week referral should be offered faster access if they were prepared to pay.
A DH spokeswoman said: 'Despite increasing demands on endoscopy services, the proportion of people waiting more than six weeks continues to fall.'
She said the DH had informed the NHS about the need to expand endoscopy services if it is to deliver improved cancer survival rates.
'It is for the local NHS to ensure it has appropriate levels of endoscopy services to meet their local healthcare needs,' she said.
'Diagnostic test waiting times will continue to form part of the performance discussions with Strategic Health Authorities.'