Sparking sharp criticism from top state and city officials wary of the University’s intentions, Harvard closed a deal Friday to purchase a 91-acre tract of land in Boston.

The land, known as Allston Landing South, which Harvard bought from the Massachusetts Turnpike Authority, includes a portion of the pike itself and the bulk of the area’s major rail yard, both of which Boston Mayor Thomas M. Menino and Mass. Secretary of State William F. Galvin say are crucial pieces of Boston infrastructure.

“Harvard should have talked to us,” an irritated Menino told The Crimson, just hours after the sale. “They told us they wanted to do it, yes—but what the future use of it is, we don’t know.”

The negotiated deal includes some guarantees that the rail yard and pike will not be affected. These guarantees including pre-existing permanent easements owned by the CSX corporation on its rail lines and by the Turnpike Authority for the pike, as well as the new easements granted to the Massachusetts Bay Transport Authority (MBTA) during the sale’s negotiation.

But officials in both the city and the state governments said those guarantees are not enough.

Menino and Galvin cited uncertainty about Harvard’s intentions for the land—as well as concerns that any changes to the pike or rail yard could hurt the area’s economy—as their main reasons for opposing the deal.

Turnpike board member Christy Mihos, who stood alone in voting against the sale in April, questioned the Turnpike Authority’s motivations in selling the land.

“We’re in the business of running a turnpike, not selling turnpike assets,” he said. “This could have some very serious effects on the turnpike. In the long term, the sale is not in the interest of toll payers or taxpayers.”

Secretary Galvin, who had originally postponed the deal on Thursday upon discovering that promised concessions for the MBTA were missing, protested that the deal would give Harvard unusual control over the land, including the potential to literally move the turnpike.

“I’m not satisfied with the deal,” Galvin declared on Friday. “It’s clear that Harvard has a very ambitious development plan for this site, and the Massachusetts Development Commission will be scrutinizing the developments as they happen.”

After Galvin postponed the deal Thursday, lawyers for Harvard, the MBTA, and the Turnpike convened overnight to seal the deal by adding the missing protections and concessions from Harvard, including space for a future MBTA track.

Nevertheless, Galvin worried about how the University’s as-yet-unannounced plans for the land could obstruct or prevent any future efforts by state officials to add a lane or make any changes to the pike.

“I remained concerned from a development point of view as to what the intentions and implications are,” Galvin added. “Harvard has said they have very long term plans but I find that hard to believe. This is not just surplus land the university is adding to its inventory for the long-distant future.”

The agreements also allow for Harvard to petition the Turnpike Authority or the MBTA to move parts or all of the roadway or the railways—although only after clearing a number of bureaucratic hurdles and gaining the approval of other state agencies.

But the University’s construction can not obstruct or complicate the activity of the turnpike or the rail yard, according to the agreement as filed at the Suffolk County Registry of Deeds.

For months, officials have challenged the sale, maintaining that the rail yard is a crucial route for freight and commuters.

Alan Stone, Harvard’s vice president of government and community affairs, indicated that notions of Harvard moving the roadway or the toll plaza were completely implausible.

“Our position all along was that we don’t want any transportation needs in the area to be compromised, and that continues to be our position,” he said.

Stone pointed to the extensive negotiation process that led to Harvard’s protection agreements for the MTA and the MBTA, which shares the railway with freight carrier CSX.

“Was it an open process, followed under law, was there public bidding, did we prevail in the bidding, were the concerns worked out?” he asks. “I think the answer to all those things is yes.”

But Menino reiterated his earlier concerns over the circumstances of the sale process, adding that he was upset over Harvard’s lack of clarity about their plans for the land.

“The thing I was upset about was that there was no process the city was considered in,” he said. “Harvard just said ‘we’re going to buy it.’ What about the future of that decision, and how does that economically impact that train yard? A lot of our product comes in through that yard.”

Menino expressed dissatisfaction with Harvard’s and the Turnpike’s engagement with City Hall.

“This is a combination of the state’s and Harvard’s fault,” he said. “There should have been more consultation with the city. We’re the ultimate agency that’s going to do the zoning of the properties. We should have part of the continual dialogue.”

Other lingering concerns about the sale to Harvard revolve around the environmental impact Harvard might have on the land, said Galvin. He pointed to the fragility of the land due to its location along the Charles River.

“As the chairman of the Massachusetts Historical Society, I’m well aware of the historical conditions of that site,” he said. “Due to a combination of institutional constructions, including [Harvard’s] new grad student housing, the river has been walled in. And the proposals would suggest a further walling in of the river.”

The 91-acre parcel is the largest underdeveloped piece of land in Boston. It augments the University’s land holdings in Boston by a third, bringing its number of acres in the city to 367.

When Harvard bought the adjacent 48-acre Allston Landing North parcel from the Turnpike in 2000, the University received the public blessing of Mayor Menino.

Except for a brief statement to the Boston Globe in April, Menino has been mostly tight-lipped in public about his concerns about the Allston land purchases.

Despite the mayor’s anger with the University’s announcement in 1997 that it had secretly purchased a large swath of land in Allston, Harvard’s relationship with City Hall has been mostly amicable in recent years. Since 1999, the University has worked on a strategic plan with the city to guide its future development in Allston.

But Menino’s dissatisfaction with Harvard’s latest purchase could mean a new hurdle in the University’s attempts to develop a good relationship with the city.

But Stone said yesterday that Harvard plans to work hard to maintain trust.

“We’ll work hard at our relationship with the mayor, we’ll work very hard,” Stone said.

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