Gov. Deval Patrick laid out his plan for restructuring Massachusetts' transportation Thursday morning in an editorial in the Boston Globe.

Patrick, a Milton Democrat, laid out his plan to consolidate transportation agencies, saying the "bureaucracy should be radically simplified."

"Multiple entities run different parts of our transportation system: the Turnpike Authority operates one highway while the Highway Department operates most others; Massport operates Logan Airport, the Tobin Bridge, and much of Boston Harbor; mass transit is divided among the MBTA and Regional Transit Authorities; DCR operates parkways," Patrick wrote. "Each has its own duplicative administrative overhead and strategy, personnel and pension systems, and maintenance programs."

Patrick noted that previous administrations left the Turnpike Authority and Massachusetts Bay Transportation Authority with $5 million in debt from the Big Dig.

"This is a sorry legacy we have inherited," Patrick said.

Patrick said the government should be looking at and planning public transportation on a system-wide basis so that travelers would be able to move from one mode of transportation to another seamlessly.

The governor wrote that the first step in this lengthy and difficult process is eliminating the Turnpike Authority. In two years, tolls on the Pike west of Route 128 will be removed, Patrick wrote, which he said cannot be used to reduce Big Dig debt on the eastern turnpike anyway.

"Restructuring the Big Dig debt will involve spreading the burden more equitably through a combination of tolls, Massport revenues, registry fees, and savings from eliminating the Turnpike Authority," Patrick wrote.

Patrick also noted that "there is simply no way around an increase in tolls in the short term. That is an unfortunate fact."

But in the long run, Patrick said he hopes to eliminate all tolls except those at the state borders and harbor tunnels.