The Virginia Supreme Court criticized Fairfax County's method of appraising commercial property yesterday, and ruled that two Skyline Plaza high-rise office buildings had been overvalued for tax purposes by $19 million over three years.

The ruling was the fourth in recent years in which the state's highest court has criticized the county's commercial real estate assessment methods.

At the heart of the case is whether the value of a commercial property depends on the actual rents and expenses of that particular building, or on typical rents and expenses for all similar commercial property in the county.

The state Supreme Court said yesterday, as it has in earlier rulings, that Fairfax County assessors depended too heavily on the higher market-value rents and expenses, and did not rely enough on the actual figures for the particular building being assessed, which were lower.

The court agreed with the owners of the two Skyline Plaza buildings at Baileys Crossroads, that their appraisals for 1980, 1981 and 1982 were too high, ordered them reduced and said the owners do not owe taxes on the overvalued part of the appraisals.

It could not be determined exactly how much of a refund the building owners will receive, but based on current tax rates it could be $250,000 to 300,000, plus interest.

A spokesman for Charles E. Smith Co., which manages the two buildings in the giant Skyline City complex, said the company would have no comment until officials study the ruling.

Fairfax County officials said yesterday that they had changed the way they appraise commercial property, and believe their current method is legal.

"We think what we are doing complies with the current law," said Robert Cherin, the senior assistant Fairfax County attorney who unsuccessfully argued the case before the high court. "We are bound by these court decisions to pay a greater degree of attention to the actual earned income of a property in the appraisal."

Cherin said officials would have to study the opinion before determining whether it would have a major impact, but he said there are no similar pending lawsuits. Even if any were filed, he said, they would affect only taxes paid since 1984 because the statute of limitations is three years.

Skyline I, completed in 1972, and Skyline II, completed in 1979, each contain about 250,000 square feet of rentable office space.

The owners, two private limited partnerships, filed suit appealing the buildings' assessed valuations for 1980, 1981 and 1982.

In 1983, Circuit Court Judge Johanna L. Fitzpatrick sent the case back to the county with an order to reevaluate the assessments. In October 1983, a month later, the county said it had reconsidered and found the original assessments to be correct. In 1984, the Circuit Court refused to reconsider, and the owners appealed.

In addition to criticizing the county's assessment method, yesterday's Supreme Court ruling said Fitzpatrick should have corrected the assessment in 1983, instead of sending the case back to the county assessment office for review.