Gov. Harry Hughes today proposed a $90 million state transportation package that meets the funding needs of Washington's Metro system, but contains a surprise element -- a car registration fee increase -- that could set off a confrontation in the legislature.

Hughes' plan abandons his long-favored idea of financing transportation programs with an increase in the gasoline tax, which has been strongly opposed by the legislature. Instead, it calls for a $5 to $8 increase in the yearly automobile registration fee and a transfer of portions of two existing taxes to the state's transportation fund.

These measures would satisfy the federal government's requirement that the state provide a stable source of Metro funds in exchange for grants to complete construction of the system. It also provides substantial money for local road programs around the stable.

Despite Hughes' apparent attempt to accomodate legislators who are opposed to increasing taxes while there is a large state surplus, his proposed rise in registration fees may incur formidable opposition from House Speaker Benjamin L. Cardin (D-Baltimore) and his colleagues from Baltimore City.

While several other legislative leaders said they found no problem with the fee proposal, the influential Cardin asserted that increasing registration fees or any other tax "is the last avenue we should look at" to fund transportation.

Cardin also said he "will have to scrutinize" Hughes' plan to return a substantial portion of the new transportation funds to each county for use at its own discretion.

Cardin said he would like the legislature to consider the auto fee increase and the new local distribution formula separately from the rest of Hughes' package. And as House majority leader Donald B. Robertson said this afternoon, "if Ben said it, it's likely to happen."

This is where the legislative confrontation is likely to arise. Some members of Hughes' staff asserted today that the transportation package -- including the proposed registration fee -- must remain intact to work.

"That is a total, intricate, interwoven package. If any piece is topped off, it will affect the others," said Michael T. Canning, one of Hughes' top aides.

The increase in registration fees which is expected to raise more than $20 million in new revenues during the next fiscal year, is needed to provide the enlarged state portion of funds for Metro operations in Montgomery and Prince George's counties, Canning said.

"If they [the legislature] drop the registration fees, there could be a problem with that," he said.

Legislators seemed divided on the issue yesterday. While Cardin expressed reservations, Senate president Jack Clark, Senate Majority Leader Harry J. McGuirk (D-Baltimore City) and House Minority Leader Raymond Beck (R-Westminster) said they had no opposition to the fee increase. "I don't think it's something that John Q. Public is going to raise a lot of hell about," said Beck.

Hughes has proposed a substantial increase in the state's share of funding Metro's operating deficit in Maryland land. Under his proposal, the share would increase from the current 40 percent to 75 percent. In fiscal 1981, the state would provide more than $26 million to the two countries, forcing them to come up with only about $10 million.

"So far we like it," said Sen. Laurence Levitan (D-Montgomery). "I don't have any problem with increased registration, but of course, some may."

The remainder of Hughes' package calls for transfering a portion of the state corporate income tax and the excise tax on cars from general revenues to the state's transportation fund, which provides money for roads and the transit system. This proposal would add about $40 million next year to that fund.

Although the two suburban Washington delegations generally were pleased with Hughes' proposal, some Prince George's senators had problems with specific portions of the plan.

Sen. Arthur Dorman (D-Prince George's) said he was disappointed that Hughes planned to continue providing 100 percent state funding for Baltimore's subway system, while providing only 75 percent to the Washington area.

"It's a question of fairness," Dorman said. "Why should we continue subsidizing them?"

Legislators generally agree that the suburban Washington and Baltimore delegations must support each other on this issue to order to pass the transportation package in the face of traditionally virulent opposition by rural legislators.