The D.C. urban renewal agency agreed yesterday to sell a parcel of land near Union Station for a new Trailways bus terminal in the same area where Greyhound paid a much higher price for a new bus depot site last year.

The Redevelopment Land Agency sold a 71,217-square-foot tract at First and L streets NE for$1,139,000--$16 a square foot--to Watergate Development Inc., of McLean. Watergate plans to build a new bus terminal for Trailways in exchange for the current Trailways terminal at 12th Street and New York Ave. NW.

Last June, Greyhound Lines Inc., paid $80 a square foot for a parcel of land about a block away at 90 K St. NE, in a swap with another developer that did not involve city property.

RLA Chairman Nira Long, when asked about the price discrepancy, said she was unaware of the earlier sale. However, housing director Robert L. Moore, who is also an RLA board member, said the Greyhound sales price was referred to in a confidential appraisal that the RLA board received for the city-owned parcel of land.

But Moore said the sales were not comparable because urban renewal land always carries with it certain restrictions that reduce the value, such as requirements for loading berths, parking spaces, and landscaping and screening. Such restrictions often do not apply to private transactions.

"We think we received a fair price," said Moore. He added that the Greyhound agreement might be "a paper transaction for them swapping one parcel of land for another . But this is a cash transaction for us."

Three veteran Washington appraisers said yesterday that land around the Trailways site had been generally selling for $10 to $12 a square foot before the Greyhound purchase, and now is selling at around $30 to $40. Greyhound officials could not be reached for further details as to why they paid $80 a square foot for their property.

While RLA's decisions to sell city-owned land are made in public, the board refuses to release the precise calculations used in determining the sales price, including the appraisals.

In March, the General Accounting Office criticized RLA for selling one of its prime downtown parcels of land for substantially less than downtown properties sold in private transactions.

According to James E. Kerr, a senior housing official, a private appraiser hired by the city set the value of the First and L streets site at $16 a square foot in December 1979, and an updated appraisal commissioned by the city earlier this month showed that there had been no change. Kerr declined to release further details of these appraisals.

Elliott Amick, an official of Watergate Development, said that after the Trailways terminal is completed his company will receive Trailways' downtown location.

Last June, Greyhound Lines Inc. announced a similar exchange with developer Morton Bender for the site of its 41-year-old downtown bus terminal. Under that agreement Bender agreed to build the bus company a new terminal at 90 K St. NE in return for the Greyhound property at 12th Street and New York Avenue NW.