The Army is leading a government review of a complex rule that environmentalists see as one of the few tools to preserve the nation's wetlands and that the Corps of Engineers sees as excessively time-consuming.

William R. Gianelli, assistant Army secretary for civil works, said the first priority of the review--prompted by the Reagan administration's second "hit list" of regulations--is to shorten the time it takes to get a corps permit to dump fill into most creeks, streams, rivers and lakes, as well as the ocean. He also wants to give the states more authority to issue permits, eliminate conflicts among various agencies and expand the use of general permits that give blanket approval to some fill activities. Some legislative changes may be needed, he said.

The current permit application process can take so long, Gianelli charged, that an applicant will feel it is "better to knuckle under to some environmental mitigation rather than live with the delay. My objective is that there be a proper balance between environmental and developmental goals."

The National Wildlife Federation's Thomas G. Tomasello thinks the desire for haste is a curious argument. "The controversies always come in large projects with a lot at stake," he said. "We need the permit program to keep federal grant/construction agencies in line alone, not to mention the private sector."

Tomasello and other environmentalists agree that the permit requirement has deterred some developers from even applying to drain and build in some of the nation's wetlands.

The permit process is regulated by the Army and the Environmental Protection Agency and by memos of understanding between the Army and agencies such as the Interior Department's Fish and Wildlife Service. The requirements are established under Section 404 of the Clean Water Act, so the permits are called "404 permits."

To get a permit for something as simple as filling in a back-yard marsh or as complicated as creating an island in the Chesapeake Bay, the applicant applies to the Army's district Corps of Engineers office. Agencies such as the EPA and the Fish and Wildlife Service are notified, a notice is placed in the Federal Register, and if there are no problems, the permit is issued.

Other federal agencies can object or recommend conditions for issuing the permit. If the objections are not met, "permit escalation" sets in. The application is bounced up the Army's chain of command as many times as the complainer--usually another federal agency--complains. Finally, in a few cases each year, the secretary of the Army must make a final decision. If the secretary issues a permit, the EPA can still intervene. Throw in a couple of environmental lawsuits and it can take a long time to get a permit.

But, Tomasello notes, that process could change without changing the regulations simply because of the new administration. With cuts in the budget and new attitudes at EPA and Interior, he said, "I don't think you're going to see the area offices of the Fish and Wildlife Service and the EPA challenging that many permits."

Lengthy cases are not that common. There are 18,000 permit applications every year and about 15,000 are approved, according to the corps. The average processing time for all permits is 130 days, but more than 10,000 are issued within 70 days.

The process gets strung out if an environmental impact statement is required, which happens only about 70 times a year, according to Army Maj. David Peixotto.

A classic "worst case," at least from the point of view of time, is that of the Hampton Roads Energy Co., which needed a permit to dispose of the dredge spoil from construction of its planned refinery on 623 acres in Portsmouth, Va., that it purchased from the Norfolk & Western Railway Co.

Hampton Roads applied for the 404 permit--one of several it needed--in 1975, but did not get it until 1979.

In the meantime, the site became extraordinarily attractive as a place to transfer coal from rail to ship. Because of clauses in the purchase contract, Norfolk & Western was able to win a court ruling that it could repurchase the land and its now completed--and valuable--federal permit package. That ruling is under appeal.

Interior, with prodding from the wildlife federation, "escalated" the permit all the way to the top. The federation's view, according to Tomasello, was not that the dredging and filling were that bad, but that tankers serving the refinery might spill oil that would destroy Chesapeake Bay shellfish beds. Because there is no appropriate "what if?" law to protect against oil spills, the fill permit process was the weapon the federation chose.

"One of the problems with 404," said EPA's William N. Hedeman Jr., who used to handle 404 cases, "is that it often rises to serve some other cause. The 404 program was enacted to deal with impacts on water quality, but the controversial cases have been on coattail issues."

Gianelli's review group includes representatives from the Office of Management and Budget, the EPA and the departments of Commerce, Justice and Interior. The Army's position will be developed and presented to the president's Task Force on Regulatory Relief early next year. In addition, four bills have been introduced in Congress that would tinker with the permit process.