Prince William County's voters yesterday rejected an attempt to move the county seat out of the city of Manassas where it has been since 1893.

The unofficial total on shifting the county courthouse to Independent Hill, a crossroads nearer the county's population center, was 8,613 against and 6,551 in favor. Proposed bond issues totalling $18.3 million to pay for a new courthouse, jail and county office building also were defeated.

Under Virginia law, no further attempt to move the courthouse may be made 10 years. The practical result of the referendum will be to fix the county center in Manassas for many years beyond that, according to both advocates and opponents of the move.

The special election, which brought out about 43 percent of the county's registered voters, included three bond issues not directly tied to the site question.

A $6.4 million bond issue for a new courthouse was defeated by a vote of 8,512 to 6,290.

A $4.7 million bond issue for a new jail was defeated 7,969 to 6,845.

A $7.2 million bond issue for new administrative offices was defeated 8,596 to 6,238.

Donald White, chairman of the Board of Supervisors and a leader in the effort to keep the courthouse in Manassas, said last night, "We did get the vote out in the western end of the county. I hope that the board will put this behind us. We need to put aside this east-west division and we have to build that jail."

It was a bitter defeat for Supervisor Alice Humphries, the moving force behind the attempt to move out of Manassas. "They swamped us in the western end with scare tactics," she said.

The debate over moving the county seat has centered publicly on the cost of the move. Opponents said a new county seat would cost far more than $18.3 million, while improving the Manassas site would cost only about $15 million. Spokesmen for the move have argued that the costs would be nearly the same either way.

But beneath that issue lay the longtime split between the rapidly developing eastern end of the county and the older western end. The supervisors divided over the move on geographic grounds except for Andrew J. Donnelly of Dumfries.

The four supervisors from the cast county, where Independent Hill is located, voted to move, with Donnelly and the two supervisors from the west voting against it. The Potomac News, located in the eastern city of Dumfries, editorialized for the shift, while the Manassas Journal Messenger opposed it.

Even the post-election parties became symbolic, with the Manassas supporters gathering at the Greater Manassas Chamber of Commerce in Manassas, and the Independent Hill backers meeting at the Eastern Prince William County Chamber of Commerce in Woodbridge.

The supervisors had been pushed into a decision on the site by the county Circuit Court. The judges had made it clear that they soon will order the board to build a jail if it does not do so on its own. They are likely to require improved court facilities.

Construction of those buildings in Manassas would make it extremely unlikely -- and expensive -- to move the courthouse to another site inthe near future.

In addition, the county administration is now operating out of 24 buildings -- half of them leased -- including an old school, former homes and converted apartment, buildings. It, too, will need new quarters before 1988.