Real made headlines when they agreed a deal to sign Kubo from FC Tokyo in 2019.
But things haven't gone as planned for the talented playmaker under former Arsenal boss Emery.
Although he has featured heavily in the Europa League, Kubo has started just one out of eight matches in La Liga.
Emery has stressed to Kubo that his time will come at the La Cerámica.
And Milla, a two-time La Liga winner with Real, insists Kubo eventually needs to play regularly for the Yellow Submarine.
"Both player and manager need to be patient," Milla told Tribalfootball.com.
"Takefusa need to play regularly to get to his true level. Time will tell what happens, as the season progresses at Villarreal."