Daniel Grabauskas, a former head of the Massachusetts Bay Transportation Authority, was formally selected Thursday to run Honolulu’s $5.27 billion rail transit project in a unanimous vote by the board of directors of the Honolulu Authority for Rapid Transportation.

Grabauskas, 48, will begin work in mid-April under a three-year contract as HART’s executive director and chief executive officer.

Keslie W.K. Hui, chairman of HART’s Human Resources Committee, said the board came to a consensus that Grabauskas is "the best fit for this project at this time" after a search that drew about 50 applicants.

Hui specifically cited Grabauskas’ communication skills, experience in running complex transportation systems and knowledge of the complex process cities must navigate to secure funding commitments from the federal government.

City officials are seeking a Full Funding Grant Agreement this year from the Federal Transit Administration to lock up $1.55 billion in federal funding. That funding is critical to the success of Honolulu’s planned 20-mile elevated rail transit line from East Kapolei to Ala Moana Center.

Grabauskas is chairman and senior strategic adviser of the Bronner Center for Transportation Management. He is also a former general manager of the Massachusetts Bay Transportation Authority, where he oversaw 6,100 employees and an annual operating budget of $1.4 billion.

Grabauskas told the HART board of directors he is pleased to be assuming control of the Honolulu project at a time when a significant number of rail construction contracts have already been awarded, and when collections for the half-percent general excise tax surcharge are running ahead of projections. The first heavy construction on the project is scheduled to begin this month.

"I’m here because I do believe this is a great project, and also because I do think that you are in a great position," he said.

However, Grabauskas warned the HART board that "unforseen circumstances are almost inevitable, particularly as the project moves into the downtown area. It’s been my experience in a very built, urban environment like Boston, as we have here with the concentration in downtown Honolulu, that there are going to be challenges."

One potential challenge is burials that could be encountered during construction in areas such as Kakaako; such finds could increase costs and delay the project.

Grabauskas said HART’s job is to mitigate those problems, be creative in developing solutions or alternatives and "be open and transparent throughout the process."

Grabauskas said after the HART meeting at the Mission Memorial Annex that he is aware that support for the rail project has faltered recently.

Former Gov. Ben Cayetano earlier this year announced he is running for Honolulu mayor, and has promised to stop the rail project if he is elected. Rail opponents have also filed federal and state lawsuits challenging the project.

"I’ve read a lot about that fact that many people say that they are for rail, but they are not for the way it’s going, and I hear that," Grabauskas said. "So what I look forward to doing is to coming here and to try to, one by one, address each of those issues so we can win those folks over to the idea that rail is actually something that can enhance the quality of their lives."

Grabauskas’ contract includes an annual base salary of $245,000 and a housing allowance of $36,000 a year. The package also includes a transportation allowance of $6,000 a year and offers Grabauskas an opportunity to earn performance bonuses of $35,000 per year.

Grabauskas was appointed general manager of the MBTA by former Massachusetts Gov. Mitt Romney.

According to published reports, Grabauskas resigned as MBTA head in August 2009 amid political pressure brought on by the new Demo­cratic administration of Gov. Deval Patrick.

Patrick questioned the agency’s leadership amid financial troubles and two crashes on one of its train lines, according to published reports. Grabauskas’ supporters characterized the move as political.

Until Thursday, HART officials had declined to disclose the names of the finalists in the search for a new executive director/CEO, but Hui identified two other finalists before the vote confirming Grabauskas.

Those finalists included HART’s acting Executive Director Toru Hamayasu and Larry Miller, former chief executive officer of transportation systems in Phoenix and British Columbia. Hui said two other finalists dropped out during the selection process. Hamayasu will stay with HART in a senior management role.