Pertinent provisions of the 2017 Rules on Administrative Cases in the Civil Service (2017 RACCS) relative to your query provide:
Section 18. Preliminary Investigation; Definition. A Preliminary Investigation is a mandatory proceeding undertaken to determine whether a prima facie case exists to warrant the issuance of a formal charge/notice of charge.
Section 19. How conducted. Preliminary investigation may be conducted in any of the following manner: a) requiring the submission of counter affidavit or comment and/or other documents from the person complained of within five (5) days from receipt of the complaint which is sufficient in form and substance; b) ex-parte evaluation of the records; or c) clarificatory meeting with the parties to discuss the merits of the case.
When the complaint is initiated by the disciplining authority, it or its authorized representative shall issue a show-cause order directing the person complained of to explain within the same period why no administrative case should be filed against the said person. The failure to submit a comment/counter-affidavit/explanation shall be considered a waiver thereof and the preliminary investigation may be completed even without the counter-affidavit/comment/explanation.
The right to counsel may be exercised even during the preliminary investigation.
For cases filed before the Commission or any of its Regional Offices, the preliminary investigation may be entrusted to lawyers of other agencies pursuant to Section 113 of these Rules.
Section 20. Duration of the Preliminary Investigation. A preliminary investigation shall commence within a non-extendible period of five (5) days upon receipt of the complaint by the disciplining authority and shall be terminated within twenty (20) days thereafter. However, the disciplining authority may extend such periods in meritorious cases.
Section 47. Formal Investigation Report. Within fifteen (15) days after the conclusion of the formal investigation, a report containing a narration of the material facts established during the investigation, the findings and the evidence supporting said findings, as well as the recommendations, shall be submitted by the hearing officer to the disciplining authority. x x x
Section 48. When Case is Decided. The disciplining authority shall decide the case within thirty (30) days from receipt of the Formal Investigation Report.
When an administrative case will be decided or resolved will depend on the circumstances of the case. The 2017 RACCS merely provides the timelines relative to the preliminary and formal investigations of the case.
On your query regarding preliminary investigation, please note that the 2017 RACCS does not explicitly provide that the complainant be furnished a copy of the comment/affidavit of the person complained of. As to the manner how preliminary investigations are conducted, the same may entail a) the submission of counter affidavit or comment and/or other documents from the person complained of; b) ex-parte evaluation of the records; or c) clarificatory meeting with the parties to discuss the merits of the case. Whatever method to employ shall be at the discretion of the disciplining authority.
Finally, we cite Section 46, paragraph 2 of the 2017 RACCS which states:
For this purpose, a pending administrative case shall be construed as such when the disciplining authority has issued a formal charge or a notice of charge to the respondent.
Hence, only those employees upon which a Formal Charge has already been issued are considered to have had a pending administrative case.