The eagles that alighted at the Navy Yard in 2007, heralding the birds' return to Philadelphia after more than two centuries, haven't visited their nest there in two years.

Unless they touch down soon - which bird experts say is unlikely - developers will cut down the tree that holds the twig aerie to make way for a new marine terminal.

But eagles, their nests, their feathers, and just about everything about them enjoy broad protection under federal laws that aim to protect the birds, which were removed from the endangered species list just three years ago.

To comply with those laws, state officials had to compensate for the expected loss of the Navy Yard nest.

"We'd like some compensation for that, for the sake of eagles and for anyone who likes to watch eagles and enjoy eagles," said Douglas Gross, the Pennsylvania Game Commission wildlife biologist who has been providing technical assistance on this issue to the U.S. Fish and Wildlife Service, which must give the permit to take the nest.

The state is proceeding to provide that compensation on two fronts. It is trying to gain control of an island that is home to an eagle's nest in the Delaware River. State officials do not want to name the island because they try to avoid disclosing where eagles live. The birds are highly sensitive to human contact and may flee their nests.

They will discuss their second front because it is already a well-known location: Pennypack Park in Northeast Philadelphia. Eagles have built a five-foot-tall nest there, hatching two young in 2009.

The state will ask a City Council committee Tuesday to add protections to that nest by enacting legislation that limits human access to it.

The legislation, which appears to represent the first time eagles that don't block and tackle have needed help from Council, would make parts of the park off-limits to human activity during nesting season from Jan. 1 through Aug. 15.

The bill also would limit construction and other activity near the nest.

Perversely, the taking of the Navy Yard nest is a sign of eagles' progress. Derided by Ben Franklin as birds of "bad moral character" because they steal fish from other birds, eagles were treated as vermin for many decades, their eggs used for decoration.

The national symbols declined after widespread use of the insecticide DDT, which caused many birds' eggshells to thin. By 1983, just three nests remained in Pennsylvania. That year, the state began a reintroduction program, releasing 88 Canadian birds over the next seven years.

Today, there are 195 nesting pairs in Pennsylvania and 84 in New Jersey. Two of those pairs are in Philadelphia. In addition to the Pennypack nest, two eagles have made a home at the John Heinz National Wildlife Refuge at Tinicum, hatching two chicks last April.

Though eagle populations are soaring, cutting down a nest, even one that appears to be abandoned, still stirs strong emotions and uncertainty.

"It's a really tricky situation because it's internationally recognized as our national symbol of freedom, and while that nest may be inactive, it has that heritage of being a bald eagle's nest," said Nate Rice, collections manager at the Academy of Natural Sciences.

He said he thought the proposed protections at Pennypack Park and the possible acquisition of the Delaware River island could compensate for the loss.

But Doug Wechsler, director of Visual Resources for Ornithology (VIREO), the academy's photograph collection, said he would have liked to see more done. The city's parks department already is required to protect the eagles at Pennypack, he said.

"The ordinance is good in that it theoretically protects the area in perpetuity," he said. "However, I question its value as mitigation, since the park should be protecting its wildlife anyway. The measures in the ordinance are things the park apparently has already been doing and should continue to do as part of their mission. To actually mitigate, they should be restoring something that has been degraded."

Debbie Beer, a Delaware County birder who first alerted state officials to the existence of the Navy Yard nest, said she and other members had lobbied the city to keep a wildlife-friendly environment there, to no avail. She has seen owls, kestrels, and other birds that she believes may leave because of the new development.

"I'm disappointed that the city doesn't see the wisdom of saving this as a green space," she said.

It is not clear how long it will take state officials to get the permit to take the Navy Yard nest or how soon the tree would be cut down after that.

No one knows what happened to the nest at that site. In spring 2007, one or more eggs hatched in that nest, and officials believe a raccoon or other predator may have eaten the eagle young.

Construction of the Southport Marine Terminal, which will include two new berths for commercial ships and, eventually, a container yard, is not expected to begin until 2013.

Sarah Nystrom, northern states bald and golden eagle coordinator for the Fish and Wildlife Service, which oversees the process for getting permits to take eagles' nests, said she thinks one is "probably likely" to be granted in this case.

Officially, the state has asked for permission to take the nest because it is in an airport flight path and eagles have posed safety risks to planes, but officials involved in the process say the marine terminal is the real driver of the request.

She was not sure how many permits had been granted nationally, but three have been granted in the northeast region, which runs from Maine to Virginia, since 2009.

Gross, of the Game Commission, said he was pleased with the plan.

"If we lose one nest here, that's a very minor setback in the scheme of bald eagle habitat protection in the state," he said. "We've done extremely well. Also, if you take the big picture, bald eagles are moving into areas where they have not nested for 200 years, so that's the historic perspective to take."

Contact staff writer Miriam Hill at 215-854-5520 or hillmb@phillynews.com.

Inquirer staff writer Sandy Bauers contributed to this article.