The former AC Milan player will remain in Melbourne for the Victory's opening A-League match against crosstown rival Melbourne City. He is expected to only join up with Cambodia during international breaks.
Victory chief executive Trent Jacobs said he was aware of Honda's desire to assist the Cambodia team during contract negotiations.
"All of our background work and all of the time we spent getting to know Keisuke demonstrated that he's a complete professional," Jacobs told the Australian Associated Press. "He has been very, very clear with us that his No. 1 priority is to come to Melbourne Victory and help us be as successful as we possibly can be.
"He knows and understands the challenge in front of him and the expectations that will be placed upon him. He's wanting to give back to football there and is clearly a really ambitious guy."