Rising to the defense of one of their region's largest industries, the Southern Governors Association today unanimously urged Congress to kill legislation that would double the federal excise tax on cigarettes.

The governors' resolution avoids any direct mention of tobacco, dwelling in general terms on the federal government's "preemption of state revenue sources," a step that some governors criticized as counter to President Reagan's New Federalism.

But from the debate, it was clear that the 12 governors were mostly concerned about the economic impact of the Senate's recent vote to raise the federal tax on cigarettes from 8 to 16 cents per pack.

"Southern states would be the biggest losers and the impact on tobacco farmers would be immense," said North Carolina's Democratic Gov. James B. Hunt, who missed the first day of the association's 48th annual meeting to attend the first tobacco auctions in his state. By industry estimates, the added federal tax will cut cigarette consumption by as much as 5 percent, triggering a drop in taxes collected by the states.

On their final day today, the Southern governors voted on 21 resolutions, some innocuous, such as promoting Miami as the site for a World Fair in 1992; some offering a regional strategy to such common problems as drug-related crime, disposal of nuclear waste and energy resources.

The governors urged Congress to make adjustments in the formulas for the federal Employment Security system, which they say discriminates against the South; to urge restrictions against foreign competitors of the domestic textile industry, a major employer in the region; and to oppose federal acid rain legislation, which the association said would "disproportionately burden" Southern states.

Republican Gov. William P. Clements of Texas introduced a resolution commending Congress and President Reagan for extending the 1964 Voting Rights Act, legislation designed to end racial discrimination at the voting booth and credited by many with changing Southern politics.

That change was evident when all but one of the 12 Southern governors today voted to endorse Clements' resolution. Republican Gov. David R. Treen of Louisiana was the lone opponent to what two decades ago was viewed as anathema to many Southern leaders.

One of the most controversial items was a proposal to move the headquarters of the association from Atlanta to the nation's capital, establishing a "Washington presence" for the governors and their states. Only Florida Gov. Bob Graham voted against the resolution, saying he didn't want the association to lose its ability to offer governors advice on state and regional -- rather than federal -- issues.

Gov. Charles S. Robb of Virginia, elected by the group today to serve as vice chairman this year (putting him in line to succeed Clements as chairman in 1983), joked that he would use his new position to "do everything I can to prohibit the association from going native" in Washington.