Head coach Kubiak suffered a 'mini-stroke' during Sunday night's loss to the Indianapolis Colts, being released from hospital on Tuesday after two days of tests.
However, with no time frame set for Kubiak's return, the franchise announced on Wednesday that defensive co-ordinator Phillips would take charge for the time being.
A statement on Texans.com read: "Defensive co-ordinator Wade Phillips was named interim head coach for Gary Kubiak who was released from Houston Methodist Hospital on Tuesday.
"Phillips is 82-61 as a head coach in his career for Dallas, Buffalo, Denver with interim stops in Atlanta and New Orleans. Any wins or losses under Phillips will officially count towards Kubiak's overall record.
"Kubiak, who is in his eighth year with the Texans, experienced a transient ischemic attack (ITA) during Sunday's game against Indianapolis. While he is expected to make a full recovery, the exact date of his return is still unknown."
Offensive co-ordinator Rick Dennison is expected to call plays, which is usually Kubiak's responsibility.
The Texans play their first game without Kubiak when they travel to the Arizona Cardinals on Sunday.