Roberts, who replaced the late William Rehnquist as Chief Justice of the United States more than three months ago, said a recent 1.9 percent increase in pay for federal judges wasn't enough.
The Los Angeles Times reports federal judges get paid 24 percent less than they did in 1969 when adjusting for inflation.
The congressional move also raised pay for military members of Congress and the executive branch.
Roberts also took to task a policy for making the federal judiciary branch pay rent when other branches of government do not.
The Defense Department doesn't pay for the Pentagon or military bases and there is no charge for prisons, embassies or congressional office buildings.
The federal judiciary uses 16 percent of its budget for rent, compared to less than .2 percent the executive branch spends.
And after a year in which a Chicago federal judge's husband and mother were murdered and a judge, court reporter and deputy were killed in a shootout in an Atlanta courthouse, Roberts asked for better protection for federal courts.