(Updated, June 8, 4:45 p.m.) — The expansion of the popular Neponset Greenway trail hit a potentially fatal roadblock this week as two state agencies stood at odds over the creation of a grade crossing at the Mattapan Square T station that is essential to the trail's construction under current plans.

The state Department of Conservation and Recreation (DCR) is attempting to extend the Greenway trail by one mile to connect the riverside path from Pope John Paul II Park to another state trail along a parkway in Hyde Park. The trail currently ends at Central Avenue in Milton.

A compromise route that has been developed over the last two years would include parts of both Milton and Boston, with part of the trail traversing the Milton side at Central Ave. before crossing over the river near the Ryan playground and heading down the Mattapan side of the river to the T station, which is the terminus of the Mattapan high-speed trolley line that runs along part of the current path. The DCR has bought a building nearby to serve as a visitors’ center for the Greenway.

“The idea was that it would allow the Mattapan community good access to the Greenway system and trail, in addition to the access Milton would have,” said Valerie Burns, president of the Boston Natural Areas Network, an advocacy group.

But MBTA officials, whose sign-off is needed for the crossing, have balked at creating a new grade crossing on their property, citing safety concerns. “This was a shock to everyone,” said Burns.

Gov. Deval Patrick, who as a Milton resident sometimes uses the current path, declined to wade in and deferred to Rich Davey, the MBTA’s general manager.

“This is a project that will benefit the neighborhood and so it’s important to engage the neighborhood, and that’s what’s been happening,” Patrick told the Reporter at a groundbreaking for a Fairmount Line commuter rail station near Codman Square. “And we’re going to get it done, and we’re going to get it done before I leave office.” Patrick has frequently said he is not seeking a third term and will leave office in 2015.

Davey said no final decision on the path has been made, “but it’s the T’s preference to work with DCR and the community to find other alternatives and there certainly have to be other alternatives other than an at-grade crossing.”

Davey said the T has safety concerns, pointing to 37 at-grade crossing accidents in the last 16 months on the Green Line and the Mattapan Line. The accidents have involved both cars and bicycles, he said, and out of the 37 accidents, 5 took place on the Mattapan Line.

“In this instance, one of several options is to direct the path over an active at-grade crossing, which is something the T has concerns [about], as would other safety agencies,” said Davey, who added that he would be meeting with local lawmakers and DCR to talk about a compromise. “We are anxious to try to work with the community and see if we can site the path [in a way] that makes sense from a safety perspective,” he said.

A DCR spokeswoman declined to provide agency officials for comment. “DCR is working closely with the MBTA on this issue, and we expect that it will be resolved soon,” said the spokeswoman, S.J. Port, in an e-mail.

MBTA officials want the path to head all the way down the river and along the current route of the trolleys, a route that would effectively cut Mattapan out of the trail, according to Burns, who found out about the MBTA decision at a meeting of Greenway supporters last week.

“I think that’s what shocked everyone is that the recommendation, or what the T is recommending, is down the alignment of the existing [trolley line] track, and no connection to Mattapan,” Burns said.

Vivien Morris, chairperson of the Mattapan Food and Fitness Coalition, also expressed surprise. “We’re really upset about it. This is an issue that’s been going on where Mattapan in particular has been given the short end of the stick for 20 years,” she said. “We felt that we were finally somewhat close to positive developments, and then to have it dismissed out of hand is worse than heartbreaking; it’s completely unfair.”

State Rep. Linda Dorcena Forry and City Councillor Charles Yancey said leaving Mattapan out of the trail was unacceptable, with Yancey calling the MBTA’s position “dead wrong.”

“I think it’s critical Mattapan is included,” said Forry, who is married to Reporter managing editor Bill Forry. “It’s not an option to leave Mattapan out.”