The Agriculture Department, with one of the poorest minority hiring records in the federal government, has slipped far behind schedule in preparing an affirmative action program for the next five years.

The department failed to meet a Dec. 31 deadline for reporting its fiscal 1987 accomplishments to the Equal Employment Opportunity Commission and now, due to bureaucratic squabbling, seems certain to miss another deadline for delivering the five-year plan.

"We have to turn out annual reports on accomplishments. And we've extended the Dec. 31 deadline to the end of January," an EEOC official said. "Chairman Clarence Thomas wants these reports out. . . . He will be happy to tell the public who is in compliance and who is not."

USDA's five-year plan, detailing departmental proposals for correcting any imbalances in the work force, is not due at the EEOC until April. But sources at USDA said that internal wrangling have delayed the project so that the deadline cannot be met.

The EEOC's latest employment statistics indicate that USDA has substantial imbalances, which in fiscal 1986 ranked it 52nd among 58 federal agencies in minority hiring. Of USDA's work force of 88,600 employees, 14.7 percent were considered minority.

Only NASA, the Interior Department and the Panama Canal Commission ranked lower than USDA in percentage of blacks in the work force. USDA was 55th in the rankings, with 8.2 percent blacks. USDA ranked 43rd for hiring women, with 34 percent, but stood 50th among the 58 on women in professional positions.

The accomplishments report for fiscal 1987, which the department has not delivered to EEOC, would have reflected any changes in these figures. USDA officials this week gave no indication when the report would be sent.

EEOC will be unable to determine whether the department met or came close to meeting goals and timetables. Because of almost constant turmoil in its civil rights and affirmative action enforcement programs since 1981, the department did not complete a required five-year plan for the 1981-1986 cycle.

Preparatory work on a new five-year plan has been stalled by squabbling between USDA lawyers and the Office of Advocacy and Enterprise (OAE), which oversees enforcement. Sources said the two sides had argued since November over wording of instructions that would go to USDA for setting goals and timetables.

An aide said Christopher Hicks, the general counsel, approved the guideline language this week. OAE chief Samuel J. Cornelius, who first said he was unaware of any delays, reported later that the guidelines will be sent around the country this week with agencies ordered to reply by Jan. 29.

Other USDA sources indicated that completion of a final plan, incorporating the targets of its various agencies, could take months. "It takes at least 90 days to draw up a good plan, but the agencies so far have had no guidance at all from Washington about what they will have to do," one source said.

Deputy Secretary Peter C. Myers, the department's equal rights overseer, said that he, too, was unaware of any delays, but that he agreed the five-year plan should be sent to EEOC on time. Myers was given his watchdog role after Secretary Richard E. Lyng, responding to the turmoil, put administrators on notice in 1986 that he would not tolerate discrimination.

Lyng acted after hearing repeated reports of upheaval in civil rights and affirmative action programs in the department. The issue came to public attention in 1981 when the director of the programs proposed that USDA become the "model" for administration plans to dismantle enforcement.

Department and administration officials denied the existence of such plans, but the USDA programs continued in turmoil, with frequent changes of directors of enforcement, a number of reorganization proposals, heavy budget cuts, curtailment of field investigations and occasional criticism from Congress.