The Interior Department agreed yesterday to give property owners along an isolated section of North Carolina's Outer Banks slightly greater acess to their property through a national wildlife refuge, but warned it will stop all traffic in three years.

The new regulations, which become effective in 30 days, are expected to do little to still the controversy over what several national conservation groups claim is the severe damage automobiles have done to the Back Bay National Wildlife Refuge in southeastern Virginia.

"I think that's an accurate statement - we're damned if we do; damned if we don't," said Fish and Wildlife Service spokesman Pat McGarvey, announcing the new rules.

The new regulations expand from six to 18 the number of hours each day in which diving on the refuge beach is permitted, allow more owners of vacation homes to make up to 30 round trips a year through the refuge and drop the $90 annual fee that the department was charging for beach travel permits.

In what conservationists considered a major victory, the Fourth U.S. Circuit Court of Appeals held in 1975 that the Interior Department could impose traffic restrictions along the refuge's ocean beach. But since then the conservationists have argued that the department has backed down from its proposed, strict traffic rules under pressure from area congressmen and the property owners.

Manyof the property owners have said they were lured to the remote Currituck County, N.C., beaches with the promise of easy access over what some advertisements called a "sand freeway" along the beachfront from Virginia Beach to North Carolina. Without the right to drive on the beach, the property owners are forced to drive about 125 miles in a roundabout route from Norfolk to their land.

Although spokesmen for Reps. G. William Whitehurst and Robert W. Daniel Jr. (R-Va.) expressed delight with the new regulations yesterday, some conservationists said they were troubled by a plan to give some part-time residents of the area acess through the refuge along with the full-time North Carolina residents.

"If they have opened it back up again, I expect our clients are going to want to go back to court," said Girard C. Larkin, a Norfolk lawyer who represented a colalition of 25 environmental groups who filed the last suit over the rules.

The Interior Department's decision to end all traffic permits along the beach by the end of 1979 was seen by most people familiar with the dispute as an effort to place pressure of North Carolina and Virginia highway officials to plan amore direct road through the area.