Two of the 12 NHS trusts which had applied for foundation status have asked for their application to be put on hold.
Bill Moyes, foundation trust regulator
North Tees and Hartlepool and Rotherham General Hospitals told officials they needed more time.
The hospitals could be included in the next wave of foundation trusts, which are due to come on stream in July.
Both trusts received three stars in last year's NHS ratings and are considered among the best in the country.
But Bill Moyes, chairman of the independent regulator for foundation trusts, which decides if hospitals can change to the new status, said the two trusts failed to show they had adequate long term plans in place.
He said: "We wanted to understand for all the applicants what sort of pressures they face, mainly financial pressures, and did they have credible strategies to tackle those.
"In terms of these two trusts, there were some questions for the long term."
The trusts will provide further information to the regulator but will not have to go to the back of the queue.
Paul Nesbitt, chief executive of Rotherham General Hospitals NHS Trust, said it needed to resolve some financial issues before becoming a foundation trust.
"We have identified further work that needs to be completed before we can confidently move forwards with our application," he said.
"There are still some financial issues relating to NHS foundation trust status that we need to understand more fully.
"We have an excellent record for achieving targets - including our financial targets - and we need to be confident that this will be maintained under NHS foundation trust status."
Mr Nesbitt said the hospital would hold talks with the regulator in the coming weeks.
"Our application remains in place," he said.
"There will be further discussions with the independent regulator during the next few weeks, before asking him to consider our application."
North Tees and Hartlepool NHS Trust said it was keen to
become a foundation trust.
"Foundation Trust status is a positive change, but also a very complex one," said a spokesman.
"We will work together with the regulator's office to gain a firmer understanding of the effects of the new funds flow and on the local health economy and primary care trusts and to also shape our business plans and service development strategy with further input from the public."