A Senate budget subcommittee voted unexpectedly today to slice all state money for Maryland's controversial automobile emissions testing program, lending new momentum to a growing effort to kill it.

The Senate subcommittee on criminal justice and transportation voted 3 to 2 to strip the $1.5 million that Gov. Harry Hughes requested for the program from the governor's proposed 1983 budget. The vote came after only a few minutes of debate, as one senator protested the move was a "back-door attempt" to repeal the program, and another argued the action would jeopardize air cleanliness.

But Sen. Victor L. Crawford (D-Montgomery), the subcommittee chairman who proposed removing the program's money, said, "The auto emissions program is a boondoggle. It won't help air quality."

A similar move to gut the program's funding is under way in the House, where a companion subcommittee will be considering the transportation budget later this week. Del. Timothy F. Maloney (D-Prince George's) said, "A clear majority of the House subcommittee favors doing the same thing.

"This is the beginning of the death knell for the program," he added.

The Senate subcommittee's vote, and the similar sentiments on the House side, represent a serious election-year revolt against Hughes and the legislative leaders, who had been negotiating a compromise plan that would please both the programs' critics and Environmental Protection Agency officials in Washington.

"The leadership had been working on a compromise," said Lou Panos, the governor's press secretary. "Whether the 3-to-2 vote by the subcommittee represents the sentiments of the full committee or of the full Senate, it's too early to say."

There was some disagreement today as to whether removing state money from the program would necessarily kill it. The state needs the $1.5 million and 30 allocated positions to pay for inspection stickers and for postage to mail out notices. The actual inspections, and the cost of buying the inspection stations and equipment, will be paid for by a private contractor.

"I think the guys on the subcommittee just misunderstood what the money was for," said Tom Widerman, associate administrator of the state's Motor Vehicles Administration. "It's kind of an irresponsible act. In effect, we'll have an inspections program but we won't have the money to pay the postage to tell people when to go."

Crawford said, however, that under Maryland law, the contract would be void if the program isn't funded and the state would not be liable for canceling the contract early.

Maloney said that cutting funds would disrupt the program, scheduled to begin next year, more effectively than voting to repeal it. Even if the legislature voted to repeal the program, he noted, Hughes could veto the repeal after the legislature adjourns in April.

Sen. Julian L. Lapides (D-Baltimore), a subcommittee member who opposed today's vote, said it was a "back-door" effort to kill the program by not paying for it.

"That's why the budget committees are the most powerful in the legislature," Lapides said. "You can emasculate any program simply by cutting the funds for it."

The inspection program, required in states with polluted air by the 1978 federal Clean Air Act, passed the Maryland legislature three years ago after being pushed by Hughes because of the threat of losing federal highway funds. The federal government has imposed sanctions on California and part of Kentucky for failing to set up programs and in Pennsylvania recently, a federal court judge ordered the state's highway funds suspended after Pennsylvania officials reneged on a court agreement to begin inspections.

In Maryland, some of the same legislators who supported the program when sanctions were threatened, have sensed a changing mood in Washington and now consider the emissions program excessive, expensive and an example of federal government interference.

The program would require $9 inspections for every Maryland-registered car and light truck less than six years old. Those who fail the inspection could be required to pay up to $75 to have their cars repaired.

The compromise worked out by Hughes and legislative leaders would reduce the inspection cost to $7.50 and lower the maximum repair cost to $50. Today, Transportation Secretary Lowell K. Bridwell said federal officials had not said whether that compromise would meet federal clean air standards.