Ellsworth II. Morse Jr., 64, an assistant comptroller general of the General Accounting Office, died Tuesday at Mount Vernon Hospital after a heart attack.

With the GAO since 1946, he had been named an assistant comptroller general in 1972. He worked in coordination with other government agencies to promote better financial management.

In 1958, Mr. Morse had served as the comptroller general's personal representative in the Joint Program to improve Accounting in the Federal Government.

Comptroller General Elmer B. Staats yesterday praised Mr. Morse and his "high professional and ethical standards." Mr. Morse "loved the GAO and was completely dedicated to its mission," Staats said.

Mr. Morse had served in various cavacities with the American Insitute of Certified Public Accountants ad was national president of the Association of Government Accountants.

He had been editor of the International Journal of Government Auditing since it was started in 1974. It is sponsored by the International Organization of Supreme Audit Institutions. He also was chairman of the board of auditors of the ogranization of American States.

The author of numerous articles for periodicals on financial subjects, Mr. Morse had received the Comptroller General's Award and the National Civil Service League Career Service Award.

Born in Shelby, Ohio, he was a graduate of Oberlin College, where he was elected to Phi Beta Kappa. He earned a master's degree from the University of Michigan and worked for the well known accounting firm of Arthur Anderson and Company in Detroit.

During World War II, Mr. Morse served as a lieutenant commander in the Navy.

Heis survived by his wife, Virginia G., of the home in Alexandria; two daughters, Mrs. Donald Yokel, of Dochester, N.Y., and Jeanne Morse, of Alexandria, and two grandchildren.