In the proposed plan, two of the buildings are around 300 ft. This designation could have serious repercussions for the $1.2 billion project and its developer, Chicago-based hotel magnate Nichjolas Pritzker.

"The FAA has been very consistent about height," Jose Juves, spokesperson for Massachusetts Port Authority, tells GlobeSt.com. "The mayor and the Boston Redevelopment Authority started to link this issue with the proposed runway, but the FAA's position has not changed. This is an attempt by City Hall to politicize this issue. What's the connection? No one ever asked City Hall for a quid pro quo."

The mayor has been a vocal supporter of the Fan Pier project and a ardent opponent of the proposed runway at Logan. The mayor's office did not return calls by presstime.

In the latest exchange, flight patterns reportedly indicate that planes are required to turn as they near the shore, taking them away from the Fan Pier buildings. Juves insists that the main concern of pilots is gaining altitude and not, as he says, "following a dotted line in the sky. These are planes flying, not railroad tracks."

Juves adds that radar tracking indicates that planes do fly over Fan Pier. "This is an attempt by the developer to create a narrowly defined portal for planes to fly through," he says. "That does not reflect the reality."

According to Juves, pilots have indicated that if the heights of the Fan Pier buildings are not lowered they will use another runway. "Logan is the fifth slowest airport in the country," he says. "This will further incapacitate it."

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