Presidential counsel Robert Lipshutz speculated yesterday that a "substantial" number of Vietnam-era veterans will have their less-than honorable administrative discharges upgraded once President Carter decides on a program to deal with military deserters.

"No definitive decision has been reached," Lipshutz told a breakfast meeting of reporters. ". . . If I were going to speculate, I'd say it would be done within the next month to six weeks."

Carter's Jan. 21 pardon of Vietnam-era draft evaders excluded more than 200,000 deserters and persons with bad discharges, who tend to poorer and more heavily black than the draft evaders.

He ordered a Defense Department study of adminsitrative discharges, those granted outside the Uniform Code of Military Justice.

Lipshutz said he, Attorney General Griffin B. Bell and Charles Kirbo, Carter's longtime friend and adviser, were asked to speed up the study.

Lipshutz said he thinks the programs' heaviest emphasis will be on servicemen with less-than-honorable discharges, and the focus will be on upgrading broad categories of such discharges rather than handling them on a case-by-case basis.

In other White House matters:

The President held his first White House meeting with a black African leader, president El Hadj Omar Bongo of the Gabonese Republic, who is to become chairman of the Organization of African Unity next year.

He announced his intention to nominate three more subcabinet officials: Gene Godley, director of the campaign advance operation for Vice President Mondale and a member of the Carter-Mondale transition staff, for assistant treasury secretary for legislative affairs; Bette B. Anderson, vice president of the Citizens and Southern National Bank in Savannah, Ga., to be a teasury under secretary; and Jay Janis, onetime chariman of Florida Gov. Reubin Askew's Housing Goals Council, to be under secretary of housing and urban development.

As the result of a review ordered by the President, the Air Force will cut 15 planes from its fleet of VIP transport aircraft stationed at Andrews Air Force Base. The move will save $6.9 million a year, and leave 44 planes available, including 13 helicopters, the White House said.

White House press secretary Jody Powell said Alabama Gov. George C. Wallace visited Carter late Wednesday. A spokesman for Wallace said the governor asked Carter's help to keep the Air Force from closing Craig AFB near Selma, by far the largest employer in the area.