Cutting a deal that clears the way for Harvard to purchase a 91-acre parcel of land in Allston, the Massachusetts Bay Transport Authority (MBTA) tentatively agreed on Thursday to drop its eminent domain claim on part of the land. But the deal is not a complete victory for the University—if it does purchase the land under these new stipulations, Harvard will have to plan around the train tracks and storage facilities that currently reside there.

The Turnpike’s decision last month to accept Harvard’s $75-million bid for the land sparked a flurry of angry letters from state and local officials—including Boston Mayor Thomas M. Menino and state transportation secretary Daniel Grabauskas—who worried that if the Turnpike sold the land to a private organization the city would lose the land’s railyard, a crucial transportation link.

The tentative new deal, which Harvard lawyers and state transportation authorities will review over the next few days, would transfer easements currently held by CSX, a private freight carrier, to the MBTA—giving the transportation agency rights to the land if CSX abandons the easements they currently hold on the parcel.

In addition to preserving the MBTA’s current use of the land for its commuter rail lines, the deal will allow the MBTA to utilize the extensive railyard on the property as a future storage facility.

Furthermore, should Harvard develop on the 91 acres of land, the MBTA will acquire a second permanent main-line track easement, as well as 20,000 additional feet of storage space. The agreement also stipulates that the University spend $1 million researching improvements that could be made to the property, like building a rail line into the Boston port.

“The MBTA is pleased with the outcome and has worked cooperatively with the Mass. Turnpike Authority to resolve the issue,” said Lydia Rivera, spokesperson for the MBTA.

Christy Mihos, a member of the Turnpike’s board, said he knew few details but welcomed the news of a deal.

“It looks like all parties came together. There’s a long-term assurance for the existence of the railway, the MBTA got what they wanted, and the city of Boston gets to keep jobs [of port and railway workers].”

But the prospect of shipping containers and trains indefinitely running through the land might make the sale less appealing to the University, which hopes to use the acreage for its long-term expansion in Allston.

Last week, Vice President for Government, Community and Public Affairs Alan J. Stone said that the University was willing to go to the table with all concerned parties.

“We’re aware in a general way in the MBTA’s interest in parts of the property,” Stone said. “As we have said before, we’re fully prepared to sit down and discuss all issues of concern.’’

But Paul Berkeley, chair of the Allston Civic Association, said that the terms of the new deal would make the land virtually unusable in the near future.

Even if CSX moves off the land, he said, the MBTA’s easement would mean that “Harvard doesn’t get to do anything but be a landlord.”

“[In the future] some different way to move freight or a different location may become available,” Berkeley said. “But right now there is no such option available.”

Last Friday MBTA officials, thinking the deal with Harvard was fast-tracked and might keep the MBTA off the land in the future, invoked eminent domain, offering the Turnpike Authority $33.25 million for the 47 acres.

Turnpike board member Mihos, who originally voted against the sale at the Turnpike’s meeting on April 10, said he was not fully satisfied with the guarded way the Turnpike has handled the land sale so far. Mihos was upset that he had only learned of the terms of the sale the night before the board voted to approve it.

“I have absolute concerns that we are not complying with the letter of the law in not having public meetings and not having minutes,” he said. “And unless this deal is in black-and-white, I still have questions about what will be done with this parcel.”

He said that the confidentiality of the Turnpike’s dealings was the primary cause of consternation amongst city and state officials.

“This administration refuses to hold open meetings,” he said, “and we get to see no documents until they are to be voted upon. It causes these blow-ups that don’t have to happen when numerous state, city and federal officials have concerns about what we’re doing in executive sessions.”

“Were talking about public policy, not a slam-bam-thank-you-ma’am deal with Harvard,” he added. “None of these concerns were being addressed. I found that troubling.”

Stone was unavailable for comment yesterday. And Director of the Allston Initiative Kathy Spiegelman declined to comment on how the deal would impact Harvard’s long-term interest in the land.

Even though the deal’s provisions significantly encumber the land in the short term, Berkeley said that Harvard’s intentions likely extend well into the long term.

“Harvard has been here for 300 years and is probably thinking 200 years ahead,” he said.

—Staff writer Alex L. Pasternack can be reached at apastern@fas.harvard.edu.

—Staff writer Lauren A.E. Schuker can be reached at schuker@fas.harvard.edu.