Louis O. Giuffrida, director of the Federal Emergency Management Agency for four embattled years, has resigned, effective Sept. 1.

Top FEMA officials have been under investigation by the Justice Department and a House oversight subcommittee because of allegations of fraud and mismanagement. The subcommittee was expected to file its report this week.

But FEMA spokesman Robert Mahaffey said yesterday that there was no connection between Giuffrida's departure and those inquiries. "He feels that he has accomplished what he set out to do when he accepted the directorship of FEMA," Mahaffey said.

In a letter sent to the White House on Tuesday night, Giuffrida said he was weighing "several opportunities from the private sector." Before he joined FEMA, Giuffrida served in the Army and California National Guard and was director of the California Specialized Training Institute. He is a close associate of Attorney General Edwin Meese III.

During Giuffrida's tenure:

*He and a subordinate came under scrutiny because the agency spent $170,000 to create a residence at FEMA's National Emergency Training Center in Emmitsburg, Md. However, Giuffrida denied that he had ever planned to put it to personal use.

*Two FEMA employes charged that Giuffrida had ordered them to award $200,000 in noncompetitive contracts to an Army friend. Giuffrida denied the allegations.

*A FEMA contractor paid a $1,480 bill for Giuffrida, another agency official and their wives to attend two political fund-raisers, and then billed the government for the events. Giuffrida testified before the House Science and Technology subcommittee on investigations and oversight that he was unaware that the contractor had paid the bills.

*The General Accounting Office found that Giuffrida improperly used his free-mail privileges to send Christmas cards to members of Congress in 1984.

*FEMA was criticized for adopting inadequate national civil defense plans and for squandering its modest budget this fiscal year to the point where cutbacks were required.

Sen. Albert Gore Jr. (D-Tenn.), who as a House member headed the subcommittee that investigated FEMA, said Giuffrida's tenure "has been riddled with controversy . . . ." He added that Giuffrida's departure "marks the end of a disastrous era for FEMA and brings hope for more competent stewardship."