The Victorian Government's plan to privatise the Port of Melbourne is floating adrift, despite a desperate bid to pass the sale bill on the last parliamentary sitting day of the year.

The Andrews Government threatened to bypass the Parliament if the legislation did not pass the Upper House on Thursday, after furious last-minute negotiations with the Opposition.

But the Government capitulated and agreed to adjourn debate on the sale of the port's long-term lease until the Parliament sits again in February.

Treasurer Tim Pallas said the Government had been unable to reach an agreement with the Coalition on issues relating to the compensation clause and the port licence fee.

"While I am disappointed that we have been unable to secure an outcome today, the Andrews Labor Government has worked hard to ensure the best possible outcome for Victorians," Mr Pallas said.

"We look forward to the Opposition sticking to their stated February timetable and respecting the mandate which we received at the last election."

A select committee recommended 15 changes to the Government's plan to reap up to $7 billion by leasing the port for 50 years, with an optional 20-year extension.

They included capping the lease at 50 years and removing the clause that would compensate the leaseholder if a rival port was developed at Hastings or Bay West.

There has also been dispute about whether annual port licence fees should be paid upfront as a lump sum.

Greens still oppose sale, Coalition confident of deal

Opposition leader Matthew Guy said he was confident the parties could strike a deal over the next two months.

"The Coalition has put forward a number of sensible suggestions to progress the bill and we acknowledge the Government has responded to the select committee's findings," Mr Guy said.

"We anticipate continuing discussions with the Government to ensure that an amended bill can pass the Parliament in February."

Greens leader Greg Barber said he remained opposed to the port's privatisation.

"It's not too late to stop this port sale," Mr Barber said.

"The evidence is mounting as to how damaging it could be to our export-oriented economy."

Labor hopes to use the proceeds of the sale, which have already been factored into the budget's bottom line, to fund the removal of 50 railway level crossings over eight years.

The Government still hopes to sell the port in the first three months of 2016.

The Victorian Parliament sits again on February 9.