The independent truck driver shutdown, apparently fueled more by fear than tax protest, began for the first time to create disruptions for shippers and markets yesterday as shooting and rock-throwing incidents continued.

Truckers hauling fish for processing to Hampton Roads, Va., discontinued service because of threats; a Florida farmers' market reported it was having trouble getting trucks to haul fresh fruit and produce, and markets in St. Louis, Boston, and New York reported they were not receiving as much produce as usual.

For the first time, Transportation Department officials monitoring the situation did not question reports that substantial numbers of truckers were declining to haul goods.

John Fowler, DOT general counsel, said, "In some places there may be some spot shortages in some commodities this weekend. But in no place that we're aware of is there a crisis shortage, nor do we find a specific commodity that isn't moving at all."

He said he thinks many truckers are declining to take second loads this week, but expects that if violence abates, "we are going to have trucks back on the road next week."

According to the Associated Press, at least 260 trucks have been hit by gunfire and 290 others have been damaged by brickbats, firebombs and other missiles or tire-slashing since the strike began at midnight Sunday. One North Carolina driver was shot and killed earlier this week.

The majority of the incidents have been in Ohio and Pennsylvania; the Northeast appears to be the section of the country most likely to suffer spot food shortages if disruptions were to become serious.

Thomas J. Callaghan, managing director of a trucking group that uses many independent drivers--those who own and operate their own rigs--said yesterday that, for first time, his members said many drivers would not work. He said a Rocky Mountain-area firm reported that two-thirds of its drivers declined to work and that as many as 35 percent at other firms were staying home.

Stanley Hamilton, executive director of another large trucking group, said that "the violence seems to have leveled off," but that the number of drivers declining to drive "is rising, particularly in Pennsylvania, Ohio and Kentucky."

"These violent incidents have gotten out on television and the CB radios," Callaghan said, "and the drivers are afraid. Nobody reports their owner-operators feel so strongly about these taxes that they're going to pay 2 1/2 years from now that that's the reason" they are staying home.

The Independent Truckers Association called the strike to protest new trucking taxes, including the 5-cent-a-gallon increase on diesel fuel that takes effect April 1. The heaviest of the new truck levies--called a use tax--does not take effect for independents until July, 1985.

The ITA claims it has 30,000 members of the 100,000 long-haul independents, which is about one-third of the total driver population. Independents haul about 90 percent of all produce and a substantial percentage of frozen goods, including meat.

The American Meat Institute said that its members "are experiencing increasing difficulties securing motor carriers who will travel in certain areas, principally between Chicago and New York . . . . Unless the violence is stopped, there will be serious disruption." However, AMI spokesman Georgiana Francisco said, there have been no disruptions in meat shipments to date.

Jim Wanko, executive vice president of the Society of American Florists, said "we're really annoyed" at reports there will be a shortage of cut flowers and roses for Valentine's Day. He said flowers were being shipped without difficulty and that they "are not going to be any more expensive or more difficult to find."

Department of Transportation officials said some shippers are diverting from truck to rail, and a check with several eastern railroads found that traffic was up slightly.