MANILA (REUTERS) - Philippine President Benigno Aquino has accepted the resignation of his health secretary over the purchase of pneumonia vaccines in 2012 which government investigators later questioned, a spokesman said on Friday.

Health Secretary Enrique Ona, who has been on leave since October, submitted his letter of resignation on Thursday even before the completion of a government inquiry into four deals at his ministry.

"The President has accepted his resignation effective today," Herminio Coloma, the president's press secretary, told reporters in a text message.

Mr Aquino was elected in 2010 on a platform of good governance and a firm stand against corruption.

In 2012, Mr Ona had authorised the purchase of 833 million pesos (S$24 million) worth of Pneumococcal Conjugate Vaccine (PCV)-10, vaccines used for the immunisation of children against pneumonia, government investigators said.

They said the health department should have bought PCV-13, a more cost-effective vaccine which could also be used for adults to prevent pneumonia.

Mr Ona, a surgeon and a kidney transplant expert, could not be reached for comment.

There was no immediate reaction from the health ministry.