After talks with Chinese Premier Li Keqiang in Beijing's Great Hall of the People, Mr Abbott said he was confident the agreement would be finalised in the next few days, in time to be signed when President Xi Jinping visits Australia for the G20 next weekend.
But he counselled those in Australia who wanted it to be perfect that they could be disappointed.
"I can't guarantee that agreement will cover all subjects in exactly the way we would like," he said.
"... We're trying to build a house. Let's build the first storey and then in a year or two, we can build a second storey and maybe even a third storey. But let's get this done."
The Prime Minister has also held talks with the United States President Barack Obama on the sidelines of the APEC summit and joined consultations on the proposed Trans-Pacific Partnership trade grouping the Americans are pushing hard.
Mr Abbott denied the proposed TPP was causing rifts among APEC's 21 member nations because it excluded China and China's rival regional proposal excluded the US.
"I think that all of us are going forward together, trying to boost free trade - whether we're trying to do it bilaterally, pluralaterally, multilaterally or indeed unilaterally," he said.
He said it was in each member country's interests that other countries advance.
Late today, the Chinese President held landmark talks with the Japanese Prime Minister Shinzo Abe, a step towards a thaw in relations which deteriorated severely in the past two years due to the two countries' territorial dispute over islands in the East China Sea.
Tomorrow, the Australian Prime Minister hopes to finally have a meeting with Russian President Vladimir Putin, the man he vowed to "shirtfront" over his lack of assistance in investigating who shot down Malaysia Airlines flight MH17 over Ukraine.
But his rhetoric has now softened.
"Russia has said it will do everything to bring the perpetrators to justice" Mr Abbott said.
"Good on Russia for saying that. And I'll just be looking for an assurance from the president that what they said then, they meant."
The string of significant meetings associated with the APEC summit - and which will continue at the East Asia Summit later this week in Burma and then at the G20 in Brisbane - strengthen the view that these annual summits are at least as valuable for their sideline bilateral opportunities as for the group meetings themselves.
