A fall, 1979, deadline for immunizing 90 per cent of american children against major diseases was set yesterday by Health, Education and Welfare Secretary Joseph A. Califano Jr.

He called on parents, doctors, corporations, unions, governors, state and local health officers and community groups to help correct what he called the country's "intolerably low levels of childhood immunizations against such preventable diseases as polio, measles, German measles, whooping cough and tetanus."

Califano appeared before an immunization conference at the National Institutes of Health to announce a childhood immunization program in the making since President Carter in his February budget revision said he would improve health programs for the young.

At the three-day conference, which ended yesterday, a National Academy of Sciences committee recommended that Sabin, live-virus vaccine remain the nation's main means of immunizing children against polio - but it said anyone who prefers the Salk killed-virus vaccine as possibel safer should be give that vaccine.

The committee also said Salk vaccine should be used for some persons with heightened susceptibility to infection, mostly those who have immune responses have been dulled by drugs.

Both vaccines are "remarkably safe" and "highly effective," the committee concluded. But the sabin vaccine - given orally rather than injected like the Salk vaccine - was called the easiest, cheapest way to immunize large numbers of children.

The committee had been asked to help decide whether Sabin vaccine should be replaced by salk vaccine because - in the summation of Dr. Bernard Greenbert of the University of North Carolina - it may itself be the cause of paralytic polio in one person for every 5 million to 10 million children vaccinated. Dr. Albert Sabin, the vaccine's developer, denies that it causes polio.

But Greenberg said any risk must be balanced against the conquest of a disease that in the early 1950s was causing 20,000 polio cases a year.

Califano called "the national failure to protect our young from preventable diseases a shocking disgrace," because "at the moment, out of 52 million children under 15, some 20 million, almost 40 per cent, are not immunized" against one or more diseases.

He urged officials of states with laws requiring shots for children entering school to enforce those laws, and he urged governors of the others - Alaska, Arkansas, Idaho, Iowa, Missouri, Montana, Vermont and Wyoming - to propose such laws to their legislatures.

He promised $19 million in federal immunization aid to states and cities in the next fiscal year, compared with $13 million this year and $4.9 million the year before.