Speaking to media outside the apartment block of New Zealand's representative to the UN, Mr Key said New Zealand was not comfortable with Assad remaining in charge of Syria for the long term.
"But what we do recognise is we've never argued he has to go immediately - we have to work our way through these issues. So we've never argued up front that there has to be a regime change but we are strongly of the view that there is no long term place for him in Syria."
He said many of the refugees flowing out of Syria were fleeing Assad as well as Islamic State and for them to return both issues had to be dealt with.
Russia has begun giving Assad military support to help it combat Islamic State. Mr Key said there was no question Russia supported Assad.
"They have a different perspective to most other countries in the world." However, he said Russia's stance on Islamic State was similar to others and it had influence over Assad. "It's going to take a whole lot of different countries with a range of both capabilities and influence to get a long term solution in Syria."
Mr Key said the meeting between Obama and Putin will be critical. The focus on Syria and the refugees over the past month meant leaders were focusing on what needed to be done to resolve the issue.
Russia is also currently the chair of the Security Council and has called a meeting of foreign ministers on the Council to discuss Syria, a meeting Murray McCully will attend tomorrow.