The White House was warned today by key state and federal officials that six months of negotiation have not resolved major philosophical disputes over President Reagan's program to return responsibilities to state and local governments.

Richard S. Williamson, the president's top negotiator on the "federalism initiative," was subjected to two hours of pointed questioning and challenge this morning at the session of the National Conference of State Legislatures.

At the heart of the debate was Reagan's longtime insistence that basic income support and welfare programs such as Aid to Families with Dependent Children (AFDC) should be moved from Washington to the states. The president's firmness on that point has snagged negotiations on the federalism initiative he introduced as his top domestic priority last Jan. 26.

Today Williamson heard Sen. David F. Durenberger (R-Minn.), the chairman of the Senate Subcommittee on Intergovernmental Relations, Democratic Gov. Scott M. Matheson of Utah, incoming chairman of the National Governors Association, and a string of state legislators tell him there was no sound philosophical basis for sending the largest cash welfare program back to the states.

Williamson, very much on the defensive throughout the discussion, conceded that "none of us feels philosophically comfortable with all the compromises," but gave no indication that Reagan would retreat from a position he has argued vehemently for more than 15 years.

He expressed the hope that "disagreements on specific parts of the package" will not reduce the impetus for the federalism initiative.

But the program has been slowed by protracted negotiations, and Williamson today offered no firm timetable on when it will go to Congress. He said a senior staff meeting on the program that had been scheduled for last Monday was canceled because of the death of the son of presidential counselor Edwin Meese III, and has not been re-scheduled.

Williamson said there were a number of "very inflexible" views to be resolved, even within the White House, but said he hoped the final version of the Reagan initiative would be ready to present to the governors at their annual meeting in Oklahoma starting Aug. 8.

Governors and legislators and local officials have been negotiating separately with Williamson and other White House aides, and none of the groups has given a final go-ahead to the evolving package.

But, if today's discussion is indicative, the philosophical lines are hardening in ways that may cloud the program's prospects in the next session of Congress, where Reagan has vowed to make it a matter of high priority again.

Durenberger, who would preside at the Senate hearings if he is reelected in November and Republicans retain Senate control, said, "We have been through six months of negotiations, and I am not happy with the outcome. . . . What sense does it make to have Social Security, Medicare, Medicaid, Food Stamps and housing assistance all at the federal level and leave dependent children with the states?"

Matheson said he and other governors were frustrated enough by the slow pace of negotiations and Reagan's apparent stubborness that they are considering withdrawing the concessions they have made and "going back to our traditional position . . . the logical position" of making all welfare a federal responsibility.

Tom Loftus, the Democratic majority leader of the Wisconsin Assembly, said Reagan's plan was "more like feudalism than federalism." The offer to federalize Medicaid, while returning AFDC to the states, would mean, he said, "You would be an American when you are poor and sick, but a Texan when you're just poor."