May the President designate an Associate Commissioner as an Acting Chairman in the absence of the regular Chairman?

No. The Constitution expressly describes all the Constitutional Commissions as “independent.” They are not under the control of the President of the Philippines in the discharge of their respective functions. Each of these Commissions conducts its own proceedings under the applicable laws and its own rules and in the exercise of its own discretion. Its decisions, orders and rulings are subject only to review on certiorari by this Court as provided by the Constitution. The choice of a temporary chairman in the absence of the regular chairman comes under that discretion. That discretion cannot be exercised for it, even with its consent, by the President of the Philippines. 

The lack of a statutory rule covering the situation at bar is no justification for the President of the Philippines to fill the void by extending the temporary designation in favor of the respondent. The situation could have been handled by the members of the Commission on Elections themselves without the participation of the President, however well-meaning. In the choice of the Acting Chairman, the members of the Commission on Elections would most likely have been guided by the seniority rule as they themselves would have appreciated it. In any event, that choice and the basis thereof were for them and not the President to make. (Brillantes vs. Yorac, G.R. No. 93867, December 18, 1990)