As New England shippers seek relief in Congress today from higher harbor maintenance taxes, officials are warning that an $80 million shortfall in collections could lead to penalties against shippers that dodge the tax.

Executives from companies including Polaroid Corp., Cambridge, Mass., and Bose Corp., Framingham, Mass., are pressing New England's congressional delegation to help roll back the value-based fee on waterborne cargo that pays for the federal government's dredging to maintain harbor depths.The assessment tripled last year. Now said to be costing Polaroid about $300 for each container of cargo, it has been blamed for driving business away to Canadian ports.

"Nobody was really aware of what they were creating," said Rod Schonland, Polaroid manager of trade and regulations, who is a member of the New England Shippers' Advisory Council.

"Certainly the effect appears to be detrimental and unfair," said one congressional source who agreed that the tax hike to 0.125 percent of the value of shipped goods falls heavily on high-tech cargoes, particularly at ports near the Canadian border.

The fee increase from 0.04 percent also has apparently led to increased tax-dodging, a situation that troubles both government officials and shippers that are paying the tax.

DuWayne Koch, senior transportation policy adviser for the U.S. Army Corps of Engineers, said collections of $480 million in calendar year 1991 fell $80 million short of projections, primarily because of non-compliance.

''I don't think we had an enforcement problem at .04 percent but we do now," Mr. Koch said. Under the new rate, the tax pays for all the corps' prior-year dredging expenditures, up from 40 percent when it was first enacted in 1986. Added costs of $45 million for the National Oceanic and Atmospheric Administration and $5 million for enforcement also are supposed to be covered by the new rate.

David A. Kahne, program manager of the user fee task force for Customs, which collects the tax, warned that shippers who duck the fee could get slapped with fines once the agency gets the enforcement funds that are included in a pending Customs modernization bill.

"We are behind the curve on audits, and when we catch up, we will catch up with a vengeance," Mr. Kahne said.

Part of the problem is that the fee is supposed to be collected on imports, exports and even domestic waterway movements including transfers from ship to barge. Customs import documentation ensures compliance on most inbound cargo, but exports and other moves may escape the tax.

"It is not fair . . . to accept a 300 percent increase while other parties openly state they will not pay it unless forced to do so," said Joan M. Padduck, president of the Coalition of New England Companies for trade and director of imports for Reebok International Ltd. of Stoughton, Mass., in a recent letter to Sen. Edward M. Kennedy.

Anne D. Aylward, maritime director of the Massachusetts Port Authority and chairman of the American Association of Port Authorities, said the law should at least be corrected to eliminate the potential for multiple taxation on the same cargo. The question of "whether we should be taxing exports at all" should also be addressed, Ms. Aylward said.

In response to charges that the dredging trust fund is running a surplus

because of the higher tax, Mr. Koch noted that the $76.6 million will be depleted quickly once NOAA withdraws its $45 million and Customs gets its $5 million for enforcement.

But Ms. Aylward argued that the estimated $10 million a year that the trust fund gets from Boston cargo far exceeds corps' spending at the port. A long- awaited $33 million dredging project scheduled to start in 1994 will be paid 65 percent by federal funds, she said.