Auditor General Charles Deguara warned of "consequences" if parliament's watchdog offices are left vacant on Thursday.
Parliament has failed to appoint a new standards commissioner and ombudsman as both sides of the house are yet to reach an agreement.
Former Standards Commissioner George Hyzler left his post at the beginning of October and joined the European Court of Auditors (ECA).
Ombudsman Anthony Mifsud has remained in the role past his term as he waits for a replacement.
The heads of the parliamentary watchdogs are appointed by a minimum of two-thirds of parliament and therefore need the support of the two political parties.
Auditor General, Charles Deguara warned of "consequences" if the roles remain vacant.
"We know what this reality can be like, this position [auditor general] had remained vacant for a year which led to certain consequences," he said.
In 2007, a disagreement between both political parties on who should take up the position meant that the outgoing auditor general Joe Galea had to stay in the role for an extra year. However, the constitution prohibits a caretaker to fulfil the full duties of the role.
"We all agree that these positions need to be filled up," he said.
He was speaking during a visit to the National Audit Office by Hyzler.
Weighing in on the matter, Hyzler said he is confident that the government and opposition will reach an agreement.
"I have a certain tie to the office so I would naturally like to see it filled," he said.
In September Hyzler had told Times of Malta it would be a grave mistake to leave the standards office empty as there was still a lot of work to be done.
Hyzler together with outgoing member of the ECA Leo Brincat made a joint visit to the National Audit Office.
In a short welcoming address, Deguara expressed appreciation to Brincat who facilitated extensive cooperation between the two auditor bodies, as he congratulated Hyzler on his new role.
Brincat said that both the NAO and the ECA should brace for more increased challenges as EU funds are set to substantially increase.
“As funds increase so does the likelihood of fraud and irregularities,” he said.