Robert Abela has said he has "full faith" in his deputy, Chris Fearne after a Pakistan newspaper claimed the health minister's political aide was given bribery payments.
The prime minister said he had spoken to the deputy prime minister on Friday following reports of the suspect payments to his former campaign manager.
"I have full faith in him," Abela told Times of Malta.
Carmen Ciantar has been suspended without pay from her role as CEO of the Foundation for Medical Services after she offered to step aside to clear her name.
According to the Pakistan Today article, Ciantar received €443,000 worth of payments from a Dubai bank, via a Panama company. The alleged payments from Gozo International Medicare - a company linked to the fraudulent Vitals hospital deal - took place before Ciantar was appointed as CEO of FMS by Fearne.
She has since asked police to investigate and offered to testify before a magistrate.
Abela said he would not comment on the claims, saying he will leave it in the hands of the magistrate.
Vitals Global Healthcare (VGH) was the company that was controversially handed a government concession to run St Luke's, Karin Grech and Gozo hospitals in a deal that was struck down by a court earlier this year.
Abela said that Ciantar went forward to the magistrate investigating the hospital concession awarded to VGH and Steward Health Care and asked for the allegations to be investigated.
"On that note, I use the same principle that I use always, I leave the magistrates to do their work with serenity," he told Times of Malta on Friday.
When pressed further, Abela said if he did comment, he would be anticipating the magistrates' work.
"Firstly, the magistrate must decide if it will accept this request, so every comment I make now is superficial."
Fearne has distanced himself from the claims.