However, neither leader gave details of the talks or when they would begin.
At a joint news conference, Hu said the security agreement with Australia would "increase our dialogue and co-operation on major regional and international issues concerning peace and development".
The annual meeting will build on increasingly close business relations between China and Australia, with China buying record amounts of natural resources from Australia to fuel its fast growing economy.
"We both believe that although China and Australia are different in terms of national conditions we do share common interests," Hu said.
China's soaring demand for resources has triggered an economic boom in Australia and Howard is keen to see that continue.
"China’s growth is not only good for China but it is good for the whole world," he told reporters after his meeting with the Chinese leader.
On Saturday Howard is also expected to hold security talks on the fringes of the Apec leaders' summit with the US and Japan - a meeting China has already criticised.
Howard said the three-way talks with George Bush and Shinzo Abe were not directed at China, whose rapid military build-up has been a source of concern in both Washington and Tokyo.
"The trilateral dialogue between Australia, Japan and the US is not directed at anyone, anymore than the strategic dialogue I have just announced between Australia and China is not directed at anyone," he said.
Officials have not given details on the particular security concerns Australia, Japan and the US will address, beyond saying they were issues of common interest.
Hu and Bush are due to meet on Thursday, when aides say the US president will thank China for its role in pressing North Korea to give up its nuclear programme, but also raise concerns about product-safety and the Chinese currency.
Bush aides say he is also keen to discuss trade and climate control with Hu, and may may even bring up reports that China's military had hacked into Pentagon computer systems.
Their meeting comes as Condoleezza Rice, the US secretary of state, rejected charges that Iraq was distracting Washington from important issues in Asia.
"The United States has been extremely involved in Asia," Rice told the Australian Broadcasting Corp.
Rice was responding to criticism earlier this week from Richard Armitage, former US deputy secretary of state, that the Bush administration had become "so preoccupied with Iraq" that it was ignoring Asia and China's growing role in the region.