Daniel Andrews has hit back at the Victorian Ombudsman after she suggested a funding shortfall for the watchdog could be linked to her investigation into branch stacking allegations in the Victorian Labor Party.

Ombudsman Deborah Glass says she was “very disappointed” to receive about $2 million less in funding this year than she did last year.

“That really effects my ability to do the job that Parliament expects from me,” she told Neil Mitchell.

“I will run a deficit if I need to. That’s what I did last year.

“I will spend the money I have to spend, but this lack of ongoing funding means I can’t do all I want to do, and I certainly can’t plan.”

Ms Glass, whose office is investigating allegations of Labor branch stacking, told The Age she hopes the funding shortfall is “not a deliberate attempt to undermine my office”.

But she told Neil Mitchell it “certainly could look that way”.

Press PLAY below for Neil Mitchell’s interview with the Ombudsman.

Daniel Andrews has vehemently denied Ms Glass’s claims, saying they are “not based in fact”.

“Those claims, that rhetoric, that commentary, has no basis in fact whatsoever,” he said.

“Not true, not factual, not accurate.”

Press PLAY below for more.