Images sent by the Korean Central News Agency show the two in a conference room looking at a screen showing weapons being fired from the Choe Hyon, a year-old naval destroyer.
Kim Jong-un watched the missile launches via video on Tuesday and underscored the need to maintain "a powerful and reliable nuclear war deterrent", KCNA reported in a dispatch that did not mention his daughter.
The girl, reportedly named Kim Ju-ae and about 13, has accompanied her father at numerous prominent events including military parades and weapons launches since late 2022.
South Korea's spy agency assessed in February that Kim Jong-un was close to designating her as his heir.
KCNA said the missiles hit target islands off North Korea's west coast.
It quoted Kim Jong-un as saying the launches were meant to demonstrate the navy's strategic offensive posture and get troops familiarised with weapons firings.
Kim Jong-un observed similar cruise missile launches from the Choe Hyon in person last week, but his daughter was not seen at that appearance.
Tuesday's missile firings came after the start of the springtime US-South Korean military drills that North Korea views as an invasion rehearsal.
Kim Jong-un's sister and senior official, Kim Yo-jong, warned the drills again reveal the US and South Korea's "inveterate repugnancy toward" North Korea.
She said North Korea will "convince the enemies of our war deterrence".
The 11-day Freedom Shield drill that began on Monday is largely a computer-simulated command post exercise and will be accompanied by a field training program.
North Korea often reacts to the two sets of training with its own weapons tests.
