"A tough start. It's always tough to start with losses. But I am really optimistic about the direction of the team," Jones, 64, told reporters.
"I know everyone is disappointed. I'm disappointed with the results but I'm not disappointed with the direction of the team," the former England and Australia coach said in Tokyo.
The comments were the Australian's first since Italy thrashed Japan 42-14 in Sapporo on Sunday and they were beaten 25-23 by Georgia the week before, after having a player sent off.
Those results followed a 52-17 drubbing in Tokyo by England -- featuring some of the players Jones coached to the 2019 World Cup final before being fired in 2022.
"We knew that post the World Cup (Japan) had an old team, and we knew we had to change the team," Jones said.
"Changing the team means you bring in younger players and they just need time, they need guidance and they need patience," he added.
Jones's first stint in charge of Japan saw him lead the Brave Blossoms to a historic win over South Africa at the 2015 World Cup in England, inspiring the movie "The Brighton Miracle".
Japan's next games will be in the new-look Pacific Nations Cup, which starts in August.
