Ivanhoe MP Craig Langdon quit on Wednesday, citing "offensive acts of disloyalty and betrayal" by Labor colleagues.
After winning the seat in 1996, he lost preselection to contest the seat at the November 27 state election to Education Minister Bronwyn Pike's former chief-of-staff Anthony Carbines.
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In a letter to the premier, Mr Langdon said he was "fairly certain" a campaign against him was led by federal MP Bill Shorten.
Mr Brumby refused to respond to Mr Langdon's claims.
"I'm not going to get into responding," he told reporters.
"I'm not going to get into a tit-for-tat. I'm not going to respond to every claim."
Mr Shorten's office has said he would not be commenting on Mr Langdon's claims.
In his letter to the premier, Mr Langdon advised Mr Brumby to consult his backbenchers rather than just telling them what the government is doing.
"It is embarrassing for MPs to `toe the government line' only to be sold out with a sudden change of policy," he said.
"Rely more on the talent you have in your marginal seat MPs rather than the young, faceless know-it-alls in your private office."
Mr Brumby said obviously Mr Langdon would have preferred to have been chosen to contest Ivanhoe at the election, but there were also personal family issues behind his decision.
"He has said some very positive things about the government but he has also provided some advice about the importance of listening to members of parliament and I would agree," he said.
"It's always important to listen to the backbenchers and to listen to members of parliament."
Mr Langdon's resignation raises the prospect of a by-election before the November 27 state election, which would cost about $350,000, a Victorian Electoral Commission spokeswoman said.
Under the Electoral Act, lower house Speaker Jenny Lindell must issue a writ for a by-election within one month of a seat becoming vacant.
Mr Brumby has spoken against running a by-election so close to the upcoming state election.

