It’s been called Rochester’s “Buffalo Billion.” But a political fight over where to headquarter a $600-million photonics center is threatening to over shadow what could be a major economic boost for the area.

“I agree this has been unseemly over the last week or so,” said State Assembly Majority Leader Joe Morelle. “But we felt it was important at the outset to make certain that the University of Rochester, RIT and the Rochester Community are full partners in this effort,” Morelle said.

Last month, Vice President Joe Biden joined Governor Cuomo in announcing the federal Department of Defense chose Rochester as the site of the Integrated Photonics Institute for Manufacturing Innovation. All involved agreed the headquarters for the center should be in Downtown Rochester, but there was disagreement about exactly where to put it.

While Morelle and the co-chairs of the Finger Lakes Regional Economic Development Council preferred the Rochester’s historic Sibley Building, Rochester business leaders and the President of SUNY Polytechnic Institute in Albany seemed to prefer the former Bausch + Lomb building now known as the Legacy Tower.

“The one thing we were troubled by, was decisions being made unilaterally by SUNY Poly in Albany about what facilities in Rochester would be used as part of this photonics center,” said Morelle

That decision seemed to come on Monday when the college announced a deal to lease 25,000 square feet of space in the aforementioned Legacy Tower. Despite complaints from Morelle and others, SUNY Polytechnic explained as the DOD contract designee, it had the power to make the decision.

University of Rochester President Joel Seligman told Time Warner Cable News Reporter Breanna Fuss, Tuesday, the announcement was “premature.”

“Let me put it this way, it was unnecessary and awkward,” Seligman said.

Seligman, believing the two colleges are “50-50” partners, said both institutions have now agreed more discussion and study is needed before they make a final decision on a site for the headquarters.

“This not necessarily the way I wanted to reach this outcome but I look forward to working with (SUNY Polytechnic Institute President) Dr. Alain Kaloyeros and the governor’s office,” Segilman said.

In a statement, Congresswoman Louise Slaughter was not so careful in her criticism of the announcement and of Kaloyeros himself.

“This dispute is not about office space. It’s about leadership of the photonics center and that Rochester-area leaders should decide where the headquarters is located. I worked for three years to achieve this and we will not be deterred by one man’s ego,” Slaughter said.

But Kaloyeros and his college’s previous choice of the Legacy Tower has powerful support as well. The President of the Rochester Business Alliance, former Lt. Governor Bob Duffy released a statement Monday supporting that option.

Tuesday afternoon, SUNY Polytechnic Institute and the University of Rochester released a joined statement saying they were on the same page and the final site for the center still has not be chosen. Morelle credits the Governor’s office for the reversal.

“I think the Governor’s office was very involved this afternoon bringing folks together and I’m grateful to them for helping us move forward on a very, very important project that we’re hopefully moving forward together on,” said Morelle.

Despite the renewed optimism, a source told Time Warner Cable News, Tuesday, the plan to move the photonics headquarters to the Legacy Tower is moving forward. Morelle acknowledged the public concern this fight has created could jeopardize the project, but remains confident it will get done.

“I think today’s joint announcement between president Seligman and Dr. Kaloyeros now paves the way for us to get down to the really important business of working on the economic transformation for Rochester,” Morelle added.