A board created by Congress to aid failing banks of the Farm Credit System (FCS) officially began operations yesterday with four system banks in need of attention.

At the same time, Frank W. Naylor Jr., chairman of the Farm Credit Administration, the system's regulator, predicted that higher farm income, rising land values and paying of loans will help the system break even for 1987 after losing $4.8 billion since 1985.

An FCS bailout passed by Congress last month and signed by President Reagan this month assures farmers will continue to have a source of credit nationwide.

A victim of high interest rates and declines in land values, the farmer-owned system posted a loss of $201 million in the first nine months of last year, but made a $4 million profit in the third quarter, the first in 2 1/2 years. Fourth-quarter figures have not been released.

Naylor said stock in four of 12 Federal Land Banks, which make farm mortgages, has fallen to or below 75 percent of value, a threshold that requires those banks to turn to the new Assistance Board. The board can distribute up to $4 billion in FCS aid raised by sale of bonds.

Naylor would not name the four banks. Experts said the list certainly includes the bank in Jackson, Miss., which froze farmers' stock last month.