Following protests from Islamic groups, Foreign Minister Sayid Hamid Albar said there should not be any speculation that Malaysia would change its policy of refusing diplomatic ties with Israel any time soon.
"We only feel that we should listen to Israelis who have views similar to ours," he was quoted as saying by the Star newspaper on Tuesday.
The three-day conference, which began on Monday, was organised by Peace Malaysia, a grouping of non-governmental organisations, and attended by delegates from the United States, Israel, India and the Middle East.
Albar said Malaysians should learn to differentiate between the Israeli government and individual Israelis.
Asked to comment on the decision by Malaysia's Islamic opposition party to boycott the gathering, he said: "Although they have decided to withdraw officially, unofficially they are here at the conference."
Albar said earlier at a lunch address that it was tough to be upbeat about the Middle East peace process after numerous breakthroughs in the past turned out to be "false dawns".
Recent developments, including a newly elected Palestinian leader and indications of increasing US engagement towards revitalising the road map, have provided some hope, he said.