"I'm anxious Malcolm Turnbull will just stuff it up", Mr Shorten is quoted as saying.
Senate powerbroker Nick Xenophon delivered a potentially fatal blow to the plebiscite on Monday, confirming his party would vote to block the bill. That leaves the opposition center-left Labor Party as the government's only hope of getting the Senate to back a popular vote on same-sex marriage.
A plebiscite, or public vote, has been criticised as a stalling technique, and for costing taxpayers in Australia estimates of hundreds of millions of dollars.
Speaking on Sunday in Melbourne, Shorten said: "We want to have marriage equality and we want to do it as quickly as possible. It's cheaper, it's quicker and at this stage it's ridiculous to be planning a February plebiscite".
"There are few things in politics that are certain, but one thing that I would say is an absolute certainty is that if the plebiscite is carried by the Australian people, same-sex marriage will be legislated for by the Australian Parliament", he said a few days before the July 2 election.
"No matter what the enabling legislation for a plebiscite looks like, the Greens will vote against it".
Ridiculing the government's policy, he said Australians faced fines for not voting in the plebiscite while Coalition MPs had pledged to abstain in a subsequent vote in Parliament.
A leading moderate within the Coalition, Senator Birmingham said a plebiscite was the "only way" for change to happen.
Newly elected Senator Derryn Hinch has also previously voiced his support for marriage equality as well as his opposition to holding a plebiscite amidst concerns a popular vote could lead to changes being voted down.
Liberal MP Warren Entsch, a longtime advocate for reform, last week vowed not to cross the floor to support a Labor bill if the plebiscite is blocked.
In addition, the public vote would be non-binding, and would have to be followed by a parliamentary vote in order to make same-sex marriage law.