The state’s top environmental regulator approved a new framework for development on 42 acres of Boston’s central waterfront and boosted The Chiofaro Cos.’ plans for a 600-foot-tall tower.

The developer plans to replace the 459,000-square-foot harbor garage on the 1.3-acre site with a mixed-use tower estimated at 900,000 square feet.

The new municipal harbor plan allows developers to build taller buildings than previously allowed under state waterfront regulations. The maximum building height on Chiofaro’s harbor garage property was 155 feet.

As public benefits to offset the height increase, Chiofaro Cos. agreed to contribute $10 million for a new “Blueway” promenade from the Rose Kennedy Greenway to the New England Aquarium and $300,000 for a new public park and upgraded ferry facilities on Long Wharf, replacing the Chart House restaurant’s parking lot.

The Boston-based Conservation Law Foundation warned this month it will challenge the decision in court, saying Beaton exceeded his legal authority. CLF also said the new rules were the outcome of private meetings that bypassed the public and a citizen advisory committee that met for three years to study the area.

In his decision issued Monday, Secretary of Energy and Environmental Affairs Matthew Beaton said public comment letters warned that “the nature and character of Boston’s waterfront was threatened by the proposed building height.”

But he noted that the $10-million contribution for the Blueway project is the largest offset by a developer “and is commensurate with the requested height difference.”

The decision clears the path for Chiofaro Cos. to begin permitting with the Boston Planning and Development Agency. The company plans to “move quickly” on the process, Chiofaro Cos.’ Rob Cardidad said today.