A UN statement released on Thursday said the flights and resulting anti-aircraft fire were "not conducive" to stability.
A day earlier Israeli fighter jets roared across Lebanon, generating sonic booms over the capital Beirut and drawing anti-aircraft fire from Lebanese Hizb Allah guerillas.
A similar call to cease the overflights was issued by the UN a week ago. The world body said it had recorded nine separate border incursions on Wednesday with warplanes flying as far north as the port city of Tripoli.
Israel has flown regular sorties over Lebanon since withdrawing its troops from the south of the country in 2000 after a 22 year occupation under pressure from attacks by Lebanese Hizb Allah guerillas, backed by Syria and Iran.
Tensions on the UN-drawn frontier known as the Blue Line have been high since earlier this month when Israel bombed what it claimed was a training camp for militants in neighbouring Syria.
Eleven anti-aircraft rounds were fired from Lebanon in response to Wednesday's overflights. No planes were hit.