Transport for the North (TfN) said its future was looking uncertain due to ministers failing to provide any clarity about its funding after the current financial year.
The transport body has urged the government to resolve the situation and allow it to continue working on plans to improve connectivity across the north and unlock economic potential.
TfN is the only statutory sub-national transport body in the country and is funded directly by the department for transport (DfT).
But northern leaders have expressed “grave concern” that with only weeks of this financial year left, TfN is still waiting for confirmation it will continue to receive funding for the next three years.
Louise Gittins, TfN vice-chair, said: “At its meeting held [on Tuesday 25 January] the TfN board expressed its grave concern at the continued lack of certainty with regards to its core funding.
“The board was concerned to note the implications this is having on TfN’s ability to deliver its agreed programme of work, and the consequential implications the continued uncertainty has for the health and well-being of staff.”
TfN employs around 120 staff with offices in Manchester and Leeds.
It works with local authorities, business leaders and the government to identify how best to direct investment in the northern transport network.
It recently launched a freight and logistics strategy and highlighted a shortage of warehousing capacity, a lack of reliable and efficient east-west connectivity and the disproportionate reliance on ports in the south of England.
A DfT spokeswoman said: “TfN’s funding will be announced in due course.
“The Secretary of State has requested an introductory meeting with [TfN chair] Lord McLoughlin to discuss a broad range of topics.”