Amid calls for national harmony in solving regional problems, three governors disagreed today over the fairness of federal spending policies and whether they unduly benefit the so-called Sunbelt.

New York Gov. Hugh L. Carey and Illinois Gov. James P. Thompson both criticized federal spending because, they said, Northern states get back far less in federal funds than they send to Washington as tax dollars. But Oklahoma Gov. David Boren disputed the "myth" that the South has "somehow benefited by oassive transfer payments - it simply isn't true.

Their comments came during the first day of public sessions of a conference on "Alternatives to Confrontation: a National Policy toward Regional Change" at the Lyndon B. Johnson School of Public Affairs at the University of Texas here. The conference has as its goald the defusing of what some have called an economic war between the states. Repeatedly, the memory of the late President was invoked, particularly his often expressed Biblical quotation: "Come let us reason together."

That spirit was perhaps best captured in an impassioned talk by Rep. Michael Harrington (D-Mass.) who asked trat those in the South have understanding for the plight of northern cities that for three decades accepted and tried to assist poor black immigrants from the south and immigrants from Puerto Rico. "What do we do? Ignore these people?" he said. We did the humane, the decent thing to do."

Harrington asked for help from the newly prospering South and West to "bail out the [Northeast] corridor" as northern tax money helped Southerners with the Tennessee Valley and Authority and westerners with their water projects.

"My central concern is the health of the whole," he said of a nation increasingly divided between so-called Sunbelt and Snowbelt regions. "We've got to take the steps and do the things that need to be done."

What needs to be done, said Carey, is for greater equality in the return of tax dollars to northern states. Carey cited as an example a recent study concluding that in 1978 only 9 per cent of the $759 million military construction budget in the coming fiscal year will be spent in 16 Northeast and Midwest states. He said, too, that from 1950 to 1976, the number of Defense Department employees in those 16 states declined by 3 per cents. It would have risen by 700,000 if jobs "were roughly proportional to population or tax burden."

In 1976, Illinois paid nearly $6 billion more in federal taxes than it received in federal benefits, said Thompson, an amount equal to 60 per cent of the state's budget. While Illinois gets back 71 cents on the dollar, New Mexico, for example gets $1.91, he said.

"I do not want defense contracts awarded on the basis of population." Thompson said, "and I certainly don't want a military installation moved to Illinois just to even things up. [But] you can't penalize us sharply in one area and then insist that we go even Steven in all the others."

But Boren of Oklahoma cited the needs of the South, where, despite new population growths and new affluence, individual income is still less than the national average by about 10 per cent. Yet, Boren said, federal grants are made at an average of $304 for every individual but at only $251 in the South and Southwest.

Despite many unmet social needs in the South, Boren said, new legislation pending in Congress to help cities with community development would disproportionately benefit the North Ninety per cent of the cities that would gain new revenue under the legislation are in the North, he said, and 2 per cent are in the south.

In a series of meetings among academic experts in two days preceding the public sessions, papers were presented on such topics as regional differences in the costs of capital, labor, land and transportation; the role of energy in the regional distribution of economic activity; the relationships of public service needs to development patterns.

The conference concludes Tuesday.