Francis A. Keating, like the other top deputy just named by Attorney General Edwin Meese III, belongs to an all-white country club, raising the prospect that both of the new Justice Department officials could face confirmation difficulties.

Keating, now assistant Treasury secretary for enforcement and tapped for the No. 3 job at Justice, listed a stock share in the Southern Hills Country Club in Tulsa, Okla., on his 1987 financial disclosure form. A club official, who did not want to give his name, confirmed that Keating is still a member of the club.It was reported last week that John Shepherd, named by Meese to fill the job of deputy attorney general the No. 2 post in the department is a member of the all-white Bellerive Country Club and the all-male Missouri Athletic Club in the St. Louis area.

Keating and Shepherd have yet to be formally nominated by President Reagan, but Meese has served notice that both will step into their new jobs on an acting basis prior to confirmation proceedings by the Senate. Keating would succeed Associate Attorney General Stephen Trott, who is leaving to become a federal appellate judge in California.