Scientists have found a deficiency of a substance that is important to the normal functioning of cells in a small study of people infected with the AIDS virus.

The finding raises the question whether a deficiency of the substance, glutathione, leads to the collapse of the immune system that characterizes AIDS, scientists from the National Institutes of Health said in a report being published today in the British journal Lancet.

The study involved 14 men who were infected with the AIDS virus but had no symptoms and 19 men who were not infected. The amount of glutathione was reduced by up to one-half the usual levels in the men infected with the AIDS virus.

''We don't know how important the finding is,'' Dr. Ronald G. Crystal, one of the authors, said in an interview.

But Dr. Crystal said his team has begun preliminary tests of the substance on a new group of eight men to determine whether glutathione somehow plays a role in the progression from infection with the AIDS virus to the disease. Goal of the Next Tests

The tests are aimed at determining the amount of glutathione that can be inhaled safely. Such tests are needed before scientists can go on to evaluate whether increasing the amounts of glutathione to correct the deficiency could halt progression of the disease.

Most deaths from AIDS result from infections caused by microbes that do not harm people in whom the immune system is functioning normally. A variety of microbes can cause such opportunistic infections.

Soon after AIDS was recognized in 1981, scientists learned that the disease knocked out a particular type of white cell known as the CD-4 lymphocyte. Since the discovery of the AIDS virus in 1984, scientists have known that it infects only about one in 100,000 CD-4 cells in the early stages of infection.

Why infection of so few cells could have such a drastic effect on the immune system has been one of the big mysteries of AIDS. Other Factors Suspected

Thus many scientists have suspected that other factors must contribute to the progressive paralysis of the immune system.

Glutathione is a peptide, a subunit of proteins, that is found throughout nature. Scientists suspect that glutathione plays an important role in the normal functioning of the immune system and of lymphocytes called natural killer cells that are essential in the body's ability to fend off invading microbes. But scientists had not focused on the role of glutathione until now.

Discovery of the deficiency came about through studies that Dr. Crystal's team undertook to better understand why the lung forms scar tissue in certain infections.

In the first phase of the study, he said, the team focused on the release of oxidants - chemicals that consume electrons - from immune cells in the lungs of people infected with the AIDS virus. One reason for such interest was that the AIDS virus seems to damage the lung even in the absence of the secondary infections that so commonly occur there.

The researchers then turned to the body's defense against oxidants. Glutathione is known to have strong anti-oxidant action. To its surprise, the N.I.H. team found a deficiency of glutathione in certain areas of the lung. In further studies, the researchers found a generalized and previously unrecognized deficiency of glutathione in the blood. Mystifying Deficiency

The reason for the deficiency is unknown. The researchers speculated that one reason is that the lymphocytes use up large amounts of glutathione.

The researchers then went on to develop an aerosolized form of glutathione that they first tested on animals and are now using on humans to determine whether it will restore the deficiency in the lung. Preliminary results hint that it does, Dr. Crystal said.

But the new study of aerosolized glutathione is difficult to carry out. In order to measure the effects of glutathione on the lung, researchers must put tubes into the windpipe of each volunteer and then squirt fluid into the lungs to collect the cells at precise intervals following inhalation of the drug.

Dr. Crystal said it would take several months to determine a dose that could be used in a further study to learn whether aerosolized glutathione could reduce the incidence of opportunistic infections among people infected with the AIDS virus and to determine whether it halts progression of AIDS.