Hospitals have been told to remain vigilant over hospital waiting times amid concerns standards could slip.
In a letter to staff, NHS chief Sir David Nicholson said there seemed to be "misunderstandings" since monitoring of the target was relaxed last year.
But he said patients still had to be seen within the 18-week target in England despite the move.
It comes as a leading health economist warned patients may end up waiting longer now the pressure was off.
Professor John Appleby, from the King's Fund, has been charting hospital waiting times since the announcement in the summer that the government would no longer centrally manage hospital waiting.
At the time, ministers suggested this did not mean hospitals should let current standards slip but just that they would not face penalties if they did.
Professor Appleby's latest analysis - published in the British Medical Journal - does not provide clear evidence that waiting is getting worse.
Waits for diagnostic tests seem to be increasing, while the numbers waiting more than 18 weeks rose, figures for December show.
However, waiting times do tend to suffer during the winter as patients are more likely to fall ill and hospitals come under pressure from problems such as flu.
Professor Appleby said it was too early to tell whether the trends were real or just related to a "seasonal effect".
But he added the relaxation of monitoring coupled with the growing financial pressures meant patients could find themselves waiting longer in the future.
"The expectation could be that waiting times start to drift up."
While the government has always maintained this should not happen, Sir David's letter does indicate that there is some concern about how NHS trusts are behaving.
The letter stated: "In my travels around the service, I have encountered some misunderstandings about the government's intentions in respect of waiting times.
"Let me be clear that the government has stated its strong support for the rights in the NHS Constitution, which established patients' right to access services within maximum waiting times or to be offered a range of alternative providers if this is not possible."
A Department of Health spokesman added: "Our modernisation plans are designed to support a culture of continuous improvement in the NHS. Sir David Nicholson's letter was a reminder to the NHS that its obligations, duties and rights, as enshrined in the NHS Constitution, remain central to the work of the service."