The Farm Credit System, the nation's largest agricultural lender, said yesterday that it lost $2.69 billion last year because declining land values and low commodity prices continued to batter the farm economy.

The loss, the largest on record for a U.S. financial institution, was the first for the farmer-owned cooperative lending network since the Great Depression. It compared with a 1984 profit of $373 million.

The Federal Farm Credit Banks Funding Corp., which raises money for the system through the sale of bonds, said in a prepared statement that the 1985 losses were in line with a third-quarter report to shareholders that warned that 1986-1987 loan losses could surpass $3 billion.

The report said that most of the 1985 loss came during the fourth quarter as system members began adding millions of dollars to their reserves to offset expected losses from the ongoing financial stress in the farm sector.

"Numerous factors, including changing governmental agricultural policies, reduced agricultural exports resulting from a strong dollar and expanded foreign agricultural capacity, high real-interest rates, abnormal weather patterns and low commodity prices have led to a near-record number of farm and ranch insolvencies," the FCS report said.

James Roll, an FCS official in New York, said that yesterday's report did not list fourth-quarter losses separately because the agency's reports included, for the first time, its 37 member banks as well as about 700 affiliated production credit associations and other units of the FCS.

Because the farm credit system lost $426.3 million in the first three quarters of the year, its annual total of $2.69 billion indicates a loss of more than $2.2 billion in the fourth quarter. Roll said the fourth-quarter loss clearly was the largest ever for a financial institution. Prior to yesterday's report, the $1.16 billion loss recorded by Continental Illinois Corp. in the second quarter of 1984 was the largest quarterly loss in U.S. banking history, The Associated Press reported.

The FCS statement also said that, by the end of last year, net loans outstanding in the system were $66.6 billion compared with $78.5 billion at the end of 1984. This is another reflection of the deterioration in the farm economy as some loans were written off and others paid off by farmers who found other financing more attractive and left the FCS.

Another indicator of stress within the system was in nonaccruing loans, which rose to $5.323 billion by the end of 1985 from $1.84 million a year earlier. At the same time, the value of property taken over by the FCS went from $505 million in 1984 to $928 million.

Troubles in the Farm Credit System, which holds about one-third of the country's $214 billion agricultural debt, led to passage last year of legislation that directed a reorganization of the FCS and held out the possibility of last-resort federal financial assistance in an effort to restore investor confidence in FCS bonds.