Honolulu Mayor Peter Carlisle today vetoed the budget approved by the City Council for the Honolulu Authority for Rapid Transit, which is scheduled to take office next week.

The rejection of the HART operating and construction budgets accounted for two of the four vetoes announced today by Carlisle.

Carlisle’s administration had objected to the budget because of language inserted that gives the City Council final authority over the spending decisions of the semiautonomous agency. Carlisle argues the charter amendment approved by voters last year to create the board, gives HART the authority to oversee all aspects of the $5.4 billion rail project.

Council Budget Chairman Ernie Martin, who is poised to become Council chairman, has expressed confidence in an override, citing the 8-1 approval vote earlier this month. A two-thirds’ vote of the nine-member Council is needed to override a veto.

Both the Council and Carlisle have said they expect the matter to go to court.

The city Rapid Transit Division, currently part of the Transportation Services Department, will move under the authority of an executive director and a 10-member appointed board when the new fiscal year begins July 1. The Council budgeted about $17.5 million for fiscal 2012.

Carlisle’s third veto was on a bill to lower a subsidy to encourage companies and nonprofit groups to recycle.

The fourth veto was of a bill authorizing reimbursement from the transit fund to the general and highway funds for rail-related expenses incurred before the creation of the transit fund in 2007.