President Reagan’s chief of staff disagreed publicly with Energy Secretary John S. Herrington, saying there will be enough money in the President’s budget to safely operate the nation’s nuclear weapons facilities. “The President has said consistently we won’t operate any of these plants unless we can operate them in a safe manner,” Kenneth M. Duberstein said on NBC-TV’s “Meet the Press.” Herrington, according to a Washington Post story, told Duberstein in a Dec. 9 letter that the Energy Department may have to close some of the plants because there will not be enough money to comply with safety and environmental laws. Herrington said the President’s proposed budget, to be submitted to Congress Jan. 9, falls short by $360 million. He told Duberstein: “I must in good conscience advise you that . . . the system will . . . be operating beyond the bounds of acceptable risk.” Duberstein, during the TV appearance, said the money needed had been found in the Energy Department’s budget.