The Food and Drug Administration yesterday announced it will begin requiring infant formula manufacturers to test the nutritional quality of their products throughout the manufacturing process, before they are shipped and during their shelf life.

The regulations--which are more stringent than for other food products--were ordered by Congress in 1980 after cans of two formulas marketed by Syntex Laboratories were found to be deficient in chloride, an essential nutrient. Last month, nearly 3 million cans of formula manufactured by Wyeth Laboratories were also recalled because they were lacking vitamin B6.

Manufacturers will have to comply with the new rules within 90 days after they are published in the Federal Register this week. An earlier FDA proposal would have given manufacturers 180 days to comply.

The regulations will require manufacturers to code each infant formula product to identify when and where it was packed and to notify the FDA 90 days before processing a new batch of infant formula so that proper nutrient and quality control can be ensured.

In addition, infant formula makers will have to assure the FDA that their products are processed according to the quality control standards. Manufacturers will have to keep quality control records for one year beyond the expected shelf life of the formula and provide them to FDA upon request.

FDA recently has come under criticism on Capitol Hill because of the time it has taken to issue the rules. FDA Commissioner Arthur Hull Hayes testified on the Hill last month that President Reagan's required "cost-benefit" analysis of pending regulations was the main reason for delay. Legally the rules could have been put in place in May, 1981.