Samuel W. Bodman, a onetime venture capitalist and business executive who served as energy secretary during the second term of President George W. Bush and who was a deputy secretary in two other Cabinet departments, died Sept. 7 at his home in El Paso. He was 79.

The cause was primary progressive aphasia, a neurological disorder, Bush said in a statement.

Dr. Bodman, a chemical engineer who once taught at the Massachusetts Institute of Technology, joined the Bush administration in 2001 as deputy commerce secretary. In 2004, he moved to the Treasury Department, where he served less than a year as deputy secretary.

He was confirmed by the Senate as energy secretary in January 2005, succeeding Spencer Abraham. Dr. Bodman managed a $23 billion budget and more than 100,000 workers at the Energy Department, which was responsible for developing and maintaining the country’s arsenal of nuclear weapons.

He kept a low profile throughout most of his four-year tenure, except in 2007, when he fired Linton F. Brooks, chief of the nuclear weapons program, over a series of security breaches.

The Energy Department’s inspector general determined that security procedures at sensitive facilities, including the Los Alamos National Laboratory in New Mexico, were “nonexistent, applied inconsistently, or not followed.”

One contractor was found with drug paraphernalia and classified information on computer flash drives at his trailer home near Los Alamos. About 1,500 Energy Department contractors had their Social Security numbers and other personal information compromised by hackers.

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Dr. Bodman also delayed plans to open a nuclear waste repository at Yucca Mountain, Nev., because of funding shortfalls.

Samuel Wright Bodman III was born Nov. 26, 1938, in Chicago. He graduated from Cornell University in 1961 and received a doctorate in chemical engineering from MIT in 1965.

While teaching at MIT from 1965 to 1970, he also worked as technical director of a venture capital firm. He later served as president of Fidelity Investments for 17 years.

From 1987 to 2001, he was chairman and chief executive of the Boston-based chemicals and manufacturing firm Cabot Corp. The company was fined several times for failing to report hazardous spills and failing to comply with federal cleanup orders.

After leaving the government in 2009, Dr. Bodman settled in Texas and Florida.

He was a member of the American Academy of Arts and Sciences and a trustee of the Isabella Stewart Gardner Museum in Boston.

His first wife, the former Elizabeth Little, died in 1982. Survivors include his wife, Diane Bodman; three children from his first marriage; two stepchildren; a brother; 13 grandchildren; and one great-grandchild.