Senator Gregorio Honasan II, chairman of the commission's health committee, said the panel had reached "a hard decision" to reject Ubial's appointment, with 13 members voting against her confirmation. He did not elaborate.
"We are deeply grateful for Secretary Ubial's service to the Health department and for epitomizing the president's malasakit (concern) through her "All for Health, towards Health for All" Philippine Health Agenda", the Palace said in a statement.
Before Ubial, the commission had rejected the appointments of Perfecto Yasay Jr.
Duterte's picks for foreign and environment ministers, Alan Peter Cayetano and Roy Cimatu, have been confirmed.
Just a couple of days before the hearing, more than 100 employees from the Philippine Health Insurance Corporation employee signed a manifesto against Ubial citing to "grave abuse of power and usurpation of authority".
The opposition were filed by Rep. Harry Roque (Kabayan party-list), lawyer Restituto Mendoza and from Potenciano Malvar, medical director of the Gen. Miguel M. Malvar Medical Foundation in Quezon City.
Ubial did not attend the plenary session where her rejection was announced by Sen.
Ubial, in response, said she was only following the Commission on Audit (COA)'s notice of disallowance on the allowances and benefits given to PhilHealth officials and employees.
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Raised against Ubial were her appointments of officers in charge in Philhealth, which is a prerogative of the President; her supposed inconsistencies during the Zika virus outbreak, and pricey foreign trips with her son.
Ubial's son Karl, had joined some of her official trips overseas, but Ubial said they personally shouldered the expenses.
Secretary Paulyn Ubial of the Department of Health became the fifth Duterte cabinet nominee to be rejected by the Commission on Appointments (CA), composed of representatives of the Senate and the House.
Before she was rejected, Ubial said she had been "positive" that CA would confirm her despite the numerous oppositions to her appointment.
"We wish Secretary Ubial well in all her future endeavors", he added.
Last week, Senator Vicente Sotto III questioned Ubial about her frequent travels overseas in just a year.
"The DoH [Department of Health] deserves a decisive leader and I call on President Duterte to appoint an exceptional doctor with proven managerial skills to head the DoH", he said.
"The success of universal health care lies in the hand of the next DOH secretary", Roque said.