Speaking at a joint press conference, Bush said that a deal was "almost reached" but went on to say "there's much to be done".
"We want Russian accession to the WTO and will continue negotiating," he said.
While relations between the two have been frosty in recent months, the Russian president looked at ease as they spoke.
Responding to questions from journalists about whether he felt let down that an agreement had not been reached, Vladimir Putin said: "It's a complex process that lasts years. I can't say that we were not expecting such a complication.
"We will continue to work, defending our interests and the interests of our growing economy."
"Although our personal relations help us work together ... they also don't stop us from defending our national interests in any sphere."
Up for discussion
Key issues on the G8 agenda are energy security and the growing violence in the Middle East.
Bush spoke about the conflict between Israel and Lebanon.
"The best way to stop the violence is for Hezbollah to lay down its arms and to stop attacking," he said. "And therefore I call upon Syria to exert influence over Hezbollah."
Bush refrained from advising Israel to curb its attacks.
Putin said that the actions of Hezbollah were "absolutely unacceptable" but said that Israel's military response should be "balanced".
"We consider Israel's concerns to be justified. But, the use of force should be balanced. In any case, bloodshed should stop as soon as possible," Putin said.
Talks on the conflict may be sensitive with Bush's stance on the issue at odds with that of Jacques Chirac, the French president, and other leaders attending the G8 summit.
Russia has signed bilateral agreements with other key trading partners and is waiting for US agreement to join the 149-member Geneva-based WTO, which sets global trade rules.
Russia is the largest economy outside the WTO.
The talks made slow progress on a few issues.
The US wants more concessions to allow US farm goods into the Russian market and wants Russia to apply stricter controls over intellectual property rights.
The two agreed to work to help secure agreement on a UN Security Council resolution condemning North Korea's recent missile tests.