A General Services Administration realty specialist in Auburn, Wash., is facing a 90-day suspension without pay for squirreling away in an office safe more than $1.5 million in checks paid to the federal government over a six-month period.

James R. Clay, a realty specialist for 18 years, locked a $1.3 million check in an office safe last August and then headed to Alaska for a two-week property survey. Clay said yesterday his superiors were aware of the check, and he thought someone had had it deposited.

But last Thursday a clerk mentioned the check, asking Clay when it would be deposited. Clay said he immediately took it to his superiors.

"It was my fault," Clay said yesterday. "There was no attempt to take any of the money or anything. It was just a mistake."

A search of the safe turned up four other checks, all of them bid deposits or final payments on government property sales supervised by Clay.

Vito T. Chiechi, head of the regional office, said, "If it was once, I could say it was just a stupid mistake, but five times?"

Clay said the four smaller checks were in the safe because, after GSA closed its regional finance office in Auburn in January, 1982, it became "standard practice" to hold bid deposits until full payment was in.

Although no fraud has been alleged, Clay has been transferred to another job pending a review that must precede the suspension.

Officials promised immediate changes in the handling of property checks to prevent a recurrence. GSA Administrator Gerald P. Carmen said he wanted an investigation of the office's management to make sure Clay, as the low man on the totem pole, wasn't being singled out.