Amongst the cuts announced in last week's emergency Budget was the closure of nine RDAs, including Yorkshire Forward, which jointly runs Print Yorkshire alongside the BPIF.
A white paper on the RDA's future will be published later this year. It is understood that they could be replaced by a central fund, which local authorities would access individually.
The RDAs are expected to continue in their current form until March 2012, while the BPIF believes that Print Yorkshire will also continue, at least, until its funding comes to an end in March 2011.
BPIF's director of corporate affairs Andy Brown said that at this stage very little was known about the project's future.
"We are in something of a state of flux," he said. "Yorkshire Forward does not know its precise position so it's difficult to know how it will affect Print Yorkshire.
"At this stage, we expect the project to continue and be transferred, however, there will probably be a reduction in funding. If it is taken on at a more local level, there could be difficulties. Of course, we are on the look out for opportunities where they present themselves."
Terry Hodgkinson, chair of Yorkshire Forward, said: "For now, it is business as usual. We are continuing to deliver our programme of work for Yorkshire and Humber and to ensure that our region’s businesses gain the support they need at this time."