The Northern Virginia Transportation Authority is raising concerns about the General Assembly’s transportation funding bill and urging Gov. Robert F. McDonnell to make changes to it.

“We ... have concerns that some provisions of the bill limit the NVTA’s ability to fully act in accordance with its authorized duties, such as allocating funds to regional transportation projects at its discretion, and setting priorities ... such as reducing delays and improving travel times, safety, and air quality,” NVTA Chairman Martin E. Nohe said in a letter sent this week to McDonnell.

The letter comes at a time when conservative critics of the $1.4 billion-a-year transportation bill have been urging McDonnell (R) , who pushed hard for a funding plan to cap his final year in office, to veto it. Attorney General Ken Cuccinelli II (R) has objected to the measure as a matter of policy, calling it a “massive tax increase.” But Cuccinelli, who is running for governor against former Democratic National Committee chairman Terry McAuliffe, a supporter of the plan, has been mum on whether he will raise any questions about its constitutionality.

In an interview Friday, Nohe said he did not think the problems identified by NVTA make the bill unconstitutional.

“But we need clarification or assistance legislatively so we can implement the plan that the General Assembly is directing us to implement,” he said.“None of this is intended to suggest we want a change in terms of what the legislation does.”

The General Assembly last month passed a funding overhaul intended to fill the state’s fast-emptying transportation coffers, mostly by raising statewide and regional tax revenues. The bill requires that the regional tax revenue raised in heavily congested Northern Virginia and Hampton Roads be spent only in those areas, and only on transportation.

Nohe said NVTA agrees with that goal, but is concerned about a provision that causes the regional taxes to expire if those funds are misspent.

“While we support the concept, we are concerned that the misdeeds of any single jurisdiction could cause the Commonwealth, the NVTA and all other jurisdictions to suffer,” he wrote. “This could put any bonds that might be supported by this revenue at risk.”

Nohe suggested that the bill be amended so that the penalty for any misappropriation is limited to the jurisdiction involved.

The NVTA identified several other issues with the bill. They include concerns that restrictions on where regional tax revenues can be spent would complicate using the money for mass transit, since Metro and Virginia Railway Express serve areas beyond the transportation authority’s boundaries.

The bill would “prohibit the new regional funding from being used for projects such as expanding a VRE storage yard or purchasing additional VRE or Metrorail cars,” Nohe wrote.

McDonnell spokesman Tucker Martin said the governor would take NVTA’s recommendations into consideration.

“We will review their suggestions and appreciate their input,” he said.