The decision was reached in an executive session.
Senator Gregorio Honasan, chairman of the commission's health committee, said it had chose to "withhold its consent" to the appointment of Ubial.
Ubial's appointment had been opposed by several parties, whose allegations she denied.
Ubial was seen wiping her tears at the end of her confirmation hearing when Honasn informed her of the committee's decision. "It's a process which must be respected", Honasan said.
Former PhilHealth Pres. and CEO, Dr. Hildegardes Dineros, surfaced Wednesday and said Ubial had lied before the CA in saying he resigned from the PhilHealth last April. He said it was a "difficult decision" for the commission to "withhold consent to the ad interim appointment" of Ubial.
Senate President Aquilino Pimentel III said that there was a motion to disapprove the ad interim appointment of Ubial as Health Secretary and there were no objections.
Francisco claimed that Ubial committed "grave abuse of power and usurpation of authority". (PhilHealth) employee Marie Fe Francisco.
"Perhaps, she should tell her son Karl not to comment because it's bad that you're doing your job in the government... and then there are bad comments on the other leaders of the country", Pacquiao said. Dineros said Ubial "asserted (her) personal agenda" and moved to oust him from his post. "I'm sure my son does not want to jeopardize my confirmation", she said. They all accused Ubial of corruption and incompetence. Duterte appointed her when he took office.
In her defense, Ubial pointed out that Malacanang Palace had approved such travels and that her family personally paid for the travel expenses of the family members.
The Commission on Appointments (CA) on Tuesday rejected the confirmation of Paulyn Ubial as Secretary of the Department of Health (DOH) after three hearings.
Dineros said he did not resign from PhilHealth as Ubial earlier claimed but that the Secretary actually plotted his ouster.
After the rejection, Philippine President Rodrigo Duterte's spokesman, Ernesto Abella, expressed regret over the congressional commission's decision.
Vice President Leni Robredo, who served as Housing Secretary and Information and Communications Technology Secretary Rodolfo Salalima resigned, while another Cabinet secretary, former Interior Secretary Ismael Sueno was sacked by Duterte amid allegations of corruption.
Last week, Senator Vicente Sotto III questioned Ubial about her frequent travels overseas in just a year.
Rep. Henry Roque called on Duterte to appoint a doctor with "proven managerial skills". "Let's not blow it a second time around".