The Narragansett Indian Tribe’s bid to acquire all of the surplus Navy land on Aquidneck Island at no charge has run into trouble already.

The Navy informed the Bureau of Indian Affairs on Friday that an application the agency recently submitted for the Narragansetts is incomplete — including substantiation for why the tribe should get the land for free — and that the bureau has only until July 10 to resubmit.

In another development, the Navy announced on Tuesday that nearly 100 acres in Portsmouth originally deemed surplus will now be withheld for possible alternative-energy initiatives, just miles from the state’s two major windmills at Portsmouth Abbey and Portsmouth High School.

The total acreage the Navy wants to unload in Rhode Island, as part of the nationwide Base Realignment and Closure initiative, is now about 260, most of it on, or with views of, Narragansett Bay. In disposing of the surplus properties, many of which are contaminated, the Navy must first consider offers by federal agencies, including Indian Affairs. But the laws extending this privilege also require the prospective owners to accept the property as-is and to pay fair market value unless that condition is waived. There are eight other requirements, too.

On Friday, Kimberly Kesler, a director in the Navy’s BRAC office, wrote that the application for the Narragansetts “does not reflect the level of analysis required to justify a transfer of excess property, nor does it commit to accept the property when offered and in its existing condition.”

Also, because a waiver from the federal Office of Management and Budget is required for the Navy to give up the land for less than fair market value, the tribe should provide a “preliminary review” by that agency, Kessler wrote.

Indians Affairs, in a June 3 letter, had asked for a deadline extension to submit a separate application for the Wampanoag Tribe of Gay Head, on Martha’s Vineyard. In her Friday letter, Kessler granted the Wampanoags until July 10 as well.

Properties that aren’t awarded to federal agencies will be advertised in the Federal Register. At that point, Portsmouth, Middletown and Newport can act on their plans for the land to be acquired for economic development in the Melville marine area, for waterfront recreation, hiking trails and a bike path.

Tina Dolen, who, as executive director of the Aquidneck Island Planning Commission, has been working with the island communities to plan for the transfer of the Navy properties, said it appears the tribes “have a tall order in less than 30 days” to make a compelling case.

When asked about the Navy’s decision not to give up two sites along the western shore of Portsmouth, both former fuel-tank farms on the inland side of Burma Road, Dolen said, “I haven’t heard a lot of disappointment.”

In June 2008, the Navy announced that it would retain 30 of the 124 acres at the two sites for potential wind or solar power projects. But Tuesday’s announcement indicated the Navy wants to keep all of it.

“Naval Station Newport is undergoing a substantial amount of growth and transformation with the arrival of new commands and personnel,” according to a news release. “The Navy has mandated renewable-energy goals and is looking for opportunities to reduce future energy costs in an environmentally friendly way. This decision provides significant options to meet these broad Navy goals at Naval Station Newport.”

Spokeswoman Lisa Rama added that “we were a little too conservative” in estimating how much land might be needed. The additional acreage “will give us the flexibility to look into these projects.”

Dolen said that Portsmouth officials have been more focused on former fuel-storage sites closer to the Melville Marine District, which offer better opportunities for economic development.

Also, she said, cheap energy for Naval Station Newport “will only enhance its competitiveness as a training center for the Navy. It’s excellent for the communities because we receive so many benefits form the fact they are here. They are the third-largest economic engine in the state.”

rsalit@projo.com